diff --git a/tools/meryl/meryl.xml b/deprecated/tools/meryl/meryl.xml
similarity index 99%
rename from tools/meryl/meryl.xml
rename to deprecated/tools/meryl/meryl.xml
index 1a9305d6065..83b5a8cf8a3 100644
--- a/tools/meryl/meryl.xml
+++ b/deprecated/tools/meryl/meryl.xml
@@ -3,10 +3,10 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro='edam_ontology' />
     <xrefs>
         <xref type="bio.tools">meryl</xref>
     </xrefs>
-    <expand macro='edam_ontology' />
     <expand macro='requirements' />
     <version_command>meryl --version</version_command>
     <command detect_errors='exit_code'><![CDATA[
@@ -21,7 +21,7 @@
             ln -s '$operation_type.input_reads' ./input.${operation_type.input_reads.ext} &&
 
             meryl
-            $operation_type.count_operations
+            $operation_type.count_operation
             k=$size
             memory=\$GALAXY_MEMORY_GB
             threads=\${GALAXY_SLOTS:-1}
@@ -148,7 +148,7 @@
                 <option value="trio-mode">Build hap-mer dbs for trios</option>
             </param>
             <when value="count-kmers">
-                <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed">
+                <param name="count_operation" type="select" label="Count operation" help="Select an operation to be executed">
                     <option value="count">Count: count the occurrences of canonical k-mers</option>
                     <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
                     <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
@@ -446,7 +446,6 @@
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="union" />
                 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -588,13 +587,13 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="3362942" delta="300" />
+                    <has_size value="3362942" delta="2000" />
                 </assert_contents>
             </output>
             <output name="read_db_hist" file="output_23.read-db.hist" />
             <output name="pat_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="120610" delta="300" />
+                    <has_size value="120610" delta="400" />
                 </assert_contents>
             </output>
             <output name="pat_db_hist" file="output_23.pat.hist" />
diff --git a/tools/meryl/.shed.yml b/tools/meryl/.shed.yml
index 92ccb006234..87b8c9256fe 100644
--- a/tools/meryl/.shed.yml
+++ b/tools/meryl/.shed.yml
@@ -1,10 +1,18 @@
-categories:
-- Assembly
+name: meryl
+owner: iuc
 description: Meryl a k-mer counter.
 long_description: |
    Meryl a k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts k-mers in lexicographical order.
-name: meryl
-owner: iuc
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl
 homepage_url: https://github.com/marbl/meryl
 type: unrestricted
+categories:
+- Assembly
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for Meryl function: {{ tool_name }}."
+suite:
+  name: "suite_meryl"
+  description: "A suite of tools that brings the Meryl project into Galaxy."
+  long_description: |
+      Meryl a k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts k-mers in lexicographical order.
diff --git a/tools/meryl/arithmetic-kmers.xml b/tools/meryl/arithmetic-kmers.xml
new file mode 100644
index 00000000000..89381fe2819
--- /dev/null
+++ b/tools/meryl/arithmetic-kmers.xml
@@ -0,0 +1,123 @@
+<tool id="meryl_arithmetic_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>apply arithmetic operations to k-mer counts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    mkdir  -p ./temp_db/ &&
+    tar -zxf $input_meryldb_02 -C ./temp_db/ &&
+    mv ./temp_db/* tmp.meryl &&
+    meryl
+    $arithmetic_operations
+    $X
+    tmp.meryl
+    output read-db.meryl &&
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
+    <inputs>
+        <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
+            <option value="increase">Increase: add x to the count of each k-mer</option>
+            <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
+            <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
+            <option value="divide">Divide: divide the count of each k-mer by x</option>
+            <option value="divide-round">Divide-round: divide the count of each k-mer by x and round the results</option>
+            <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option>
+        </param>
+        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset"/>
+        <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand"/>
+    </inputs>
+    <outputs>
+        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="X" value="100000"/>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="arithmetic_operations" value="increase"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="59500" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="X" value="100"/>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="arithmetic_operations" value="decrease"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="42313" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="X" value="3"/>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="arithmetic_operations" value="multiply"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="60530" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="X" value="2"/>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="arithmetic_operations" value="divide"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="56200" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="X" value="2"/>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="arithmetic_operations" value="divide-round"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="56100" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="X" value="3"/>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="arithmetic_operations" value="modulo"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="37501" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool applies arithmetic operations on k-mer counts: 
+
+- Increase: add x to the count of each k-mer
+- Decrease: subsctract x from the count of each k-mer
+- Multiply: multiply the count of each k-mer by x
+- Divide: divide the count of each k-mer by x
+- Divide-round: divide the count of each k-mer by x and round th results
+- Modulo: set the count of each k-mer to the remainder of the count divided by x
+        </help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/meryl/count-kmers.xml b/tools/meryl/count-kmers.xml
new file mode 100644
index 00000000000..fc1c5d2940e
--- /dev/null
+++ b/tools/meryl/count-kmers.xml
@@ -0,0 +1,122 @@
+<tool id="meryl_count_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>count k-mers</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    #if $options_kmer_size.kmer_size == 'estimate'
+        #from math import log
+        #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4))
+    #elif $options_kmer_size.kmer_size == 'provide'
+        #set size=$options_kmer_size.input_kmer_size
+    #end if
+    ln -s '$input_reads' ./input.${input_reads.ext} &&
+
+    meryl
+    $count_operation
+    k=$size
+    memory=\$GALAXY_MEMORY_GB
+    threads=\${GALAXY_SLOTS:-1}
+    ./input.${input_reads.ext}
+    output read-db.meryl &&
+    echo 'K-mer size: ${size}' &&
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
+    <inputs>
+        <param name="count_operation" type="select" label="Count operations" help="Select an operation to be executed">
+            <option value="count">Count: count the occurrences of canonical k-mers</option>
+            <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
+            <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
+        </param>
+        <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format."/>
+        <conditional name="options_kmer_size">
+            <param name="kmer_size" type="select" label="K-mer size selector">
+                <option value="provide">Set a k-mer size</option>
+                <option value="estimate">Estimate the best k-mer size</option>
+            </param>
+            <when value="provide">
+                <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).."/>
+            </when>
+            <when value="estimate">
+                <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
+                <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="options_kmer_size">
+                <param name="kmer_size" value="provide"/>
+                <param name="input_kmer_size" value="7"/>
+            </conditional>
+            <param name="input_reads" value="child.fasta"/>
+            <param name="count_operation" value="count"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="22152" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="K-mer size: 7"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="options_kmer_size">
+                <param name="kmer_size" value="provide"/>
+                <param name="input_kmer_size" value="7"/>
+            </conditional>
+            <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz"/>
+            <param name="count_operation" value="count"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="22200" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="K-mer size: 7"/>
+            </assert_stdout>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="options_kmer_size">
+                <param name="kmer_size" value="provide"/>
+                <param name="input_kmer_size" value="7"/>
+            </conditional>
+            <param name="input_reads" value="child.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="count_operation" value="count"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="22200" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="K-mer size: 7"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool can be used to count kmers. 
+
+- Count: count the occurrences of canonical k-mers
+- Count-forward: count the occurreces of forward k-mers
+- Count-reverse: count the occurreces of reverse k-mers
+        </help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/meryl/filter-kmers.xml b/tools/meryl/filter-kmers.xml
new file mode 100644
index 00000000000..ec96677dd0d
--- /dev/null
+++ b/tools/meryl/filter-kmers.xml
@@ -0,0 +1,134 @@
+<tool id="meryl_filter_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>filter k-mers</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    mkdir  -p ./temp_db/ &&
+    tar -zxf $input_meryldb_02 -C ./temp_db/ &&
+    mv ./temp_db/* tmp.meryl &&
+    meryl
+    $filter_operations
+    #if $filter_type.type == 'times'
+        $filter_type.N
+    #elif $filter_type.type == 'frequency'
+        distinct=${operation_type.filter_type.distinct}
+    #end if
+    tmp.meryl
+    output read-db.meryl &&
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
+    <inputs>
+        <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed">
+            <option value="less-than">Less-than: return k-mers that occur fewer than a threshold value</option>
+            <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option>
+            <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option>
+            <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option>
+        </param>
+        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset"/>
+        <conditional name="filter_type">
+            <param name="type" type="select" label="Type of filtering">
+                <option value="times">Return k-mers that occur N times in the input</option>
+                <option value="frequency">Return k-mers occurring at specific frequencies</option>
+            </param>
+            <when value="times">
+                <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input."/>
+            </when>
+            <when value="frequency">
+                <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="filter_type">
+                <param name="N" value="100"/>
+            </conditional>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="filter_operations" value="less-than"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="32077" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="filter_type">
+                <param name="N" value="80"/>
+            </conditional>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="filter_operations" value="greater-than"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="49643" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="filter_type">
+                <param name="distinct" value="0.9998"/>
+            </conditional>
+            <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb"/>
+            <param name="filter_operations" value="greater-than"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="1634" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="filter_type">
+                <param name="N" value="100"/>
+            </conditional>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="filter_operations" value="equal-to"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="2621" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="filter_type">
+                <param name="N" value="100"/>
+            </conditional>
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <param name="filter_operations" value="not-equal-to"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="59100" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool can be used to filter k-mers.
+
+- Less-than: return k-mers that occur fewer than N times in the input
+- Greater-than: return k-mers that occur more than N times in the input
+- Equal-to: return k-mers that occur exactly N times in the input
+- Not-equal-to: return k-mers that do not occur exactly N times in the input
+
+        </help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/meryl/groups-kmers.xml b/tools/meryl/groups-kmers.xml
new file mode 100644
index 00000000000..9306b36bfdf
--- /dev/null
+++ b/tools/meryl/groups-kmers.xml
@@ -0,0 +1,174 @@
+<tool id="meryl_groups_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>apply operations on k-mer databases</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    #for $i,$mdb in enumerate($input_meryldb_02)
+        mkdir -p ./tmp_folder_$i/ &&
+        tar -zxf $mdb -C ./tmp_folder_$i &&
+        mv ./tmp_folder_$i/* db_'${i}'.meryl &&
+    #end for
+    meryl $groups_operations output read-db.meryl db_*  &&
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
+    <inputs>
+        <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
+            <option value="union">Union: return k-mers that occur in any input</option>
+            <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
+            <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>
+            <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option>
+            <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option>
+            <option value="intersect-min">Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count</option>
+            <option value="intersect-max">Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count</option>
+            <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option>
+            <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option>
+            <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option>
+            <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option>
+        </param>
+        <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb"/>
+    </inputs>
+    <outputs>
+        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="union"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="36100" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="union-min"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="58925" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="union-max"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="58930" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="union-sum"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="58600" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="intersect"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="14951" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="intersect-min"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="14957" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="intersect-max"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="14956" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="intersect-sum"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="14953" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="subtract"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="23999" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="difference"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="24016" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
+            <param name="groups_operations" value="symmetric-difference"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="57455" delta="1000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. Apply operations on multiple k-mer databases.
+
+- Union-min: return k-mers that occur in any input, set the count to the minimum count
+- Union-max: return k-mers that occur in any input, set the count to the maximum count
+- Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
+- Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
+- Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
+- Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
+- Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
+- Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
+- Difference: return k-mers that occur in the first input, but none of the other inputs
+- Symmetric-difference: return k-mers that occur in exactly one input
+
+        </help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/meryl/histogram-kmers.xml b/tools/meryl/histogram-kmers.xml
new file mode 100644
index 00000000000..3749c199a16
--- /dev/null
+++ b/tools/meryl/histogram-kmers.xml
@@ -0,0 +1,40 @@
+<tool id="meryl_histogram_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>get k-mer frequency histogram</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    mkdir  -p ./temp_db/ &&
+    tar -zxf $input_meryldb_02 -C ./temp_db/ &&
+    mv ./temp_db/* tmp.meryl &&
+    meryl histogram tmp.meryl > read-db.hist
+    ]]></command>
+    <inputs>
+        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb"/>
+    </inputs>
+    <outputs>
+        <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
+            <output name="read_db_hist" file="output_24.read-db.hist"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool determines a k-mer frequency histogram.
+        </help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/meryl/macros.xml b/tools/meryl/macros.xml
index 85d23f65a6c..77ce65b497c 100644
--- a/tools/meryl/macros.xml
+++ b/tools/meryl/macros.xml
@@ -2,6 +2,7 @@
     <token name="@TOOL_VERSION@">1.3</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
     <token name="@SUFFIX_VERSION@">6</token>
+    <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0196</edam_topic>
@@ -17,6 +18,19 @@
             <requirement type="package" version="1.34">tar</requirement>
         </requirements>
     </xml>
+    <xml name="meryldb_archive_assumptions">
+        <has_archive_member path="^[^/]+.meryl$" n="1"/>  <!-- folder also counts -->
+        <has_archive_member path="[^/]+.meryl/merylIndex" n="1" all="true">
+            <has_size min="1"/>
+        </has_archive_member>
+        <has_archive_member path="[^/]+.meryl/.*\.merylIndex" n="64" all="true">
+            <has_size min="1"/>
+        </has_archive_member>
+        <has_archive_member path="[^/]+.meryl/.*\.merylData" n="64" all="true">
+            <!-- <has_size min="1"/> seems to be 0 sometimes -->
+        </has_archive_member>
+        <has_archive_member path=".*" n="130"/>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">                                                                   
diff --git a/tools/meryl/print.xml b/tools/meryl/print.xml
new file mode 100644
index 00000000000..e4156bad517
--- /dev/null
+++ b/tools/meryl/print.xml
@@ -0,0 +1,41 @@
+<tool id="meryl_print" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>get k-mer counts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    mkdir  -p ./temp_db/ &&
+    tar -zxf $input_meryldb_02 -C ./temp_db/ &&
+    mv ./temp_db/* tmp.meryl &&
+    meryl print tmp.meryl > read-db.tabular
+    ]]></command>
+    <inputs>
+        <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb"/>
+    </inputs>
+    <outputs>
+        <data name="read_db_print" format="tabular" from_work_dir="read-db.tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb"/>
+            <output name="read_db_print" file="output_25.read-db.tabular" sort="true"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool gets the k-mer counts as a table.
+
+        </help>
+    <expand macro="citations"/>
+</tool>
diff --git a/tools/meryl/test-data/child.fastq.gz b/tools/meryl/test-data/child.fastq.gz
new file mode 100644
index 00000000000..45d49c530e8
Binary files /dev/null and b/tools/meryl/test-data/child.fastq.gz differ
diff --git a/tools/meryl/trio-mode.xml b/tools/meryl/trio-mode.xml
new file mode 100644
index 00000000000..3cde73cb5b0
--- /dev/null
+++ b/tools/meryl/trio-mode.xml
@@ -0,0 +1,146 @@
+<tool id="meryl_trio_mode" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
+    <description>build hap-mers databases for trios</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">meryl</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>meryl --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
+    #if $options_kmer_size.kmer_size == 'estimate'
+        #from math import log
+        #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4))
+    #elif $options_kmer_size.kmer_size == 'provide'
+        #set size=$options_kmer_size.input_kmer_size
+    #end if
+    #for $i, $read in enumerate($paternal_reads):
+        mkdir 'paternal${i}.meryl' &&
+        ln -s '$read' ./input_paternal_${i}.${read.ext} &&
+        meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_paternal_${i}.${read.ext} output 'paternal${i}.meryl' &&
+    #end for
+    meryl union-sum paternal*.meryl output pat.meryl &&
+    #for $i, $read in enumerate($maternal_reads):
+        mkdir 'maternal${i}.meryl' &&
+        ln -s '$read' ./input_maternal_${i}.${read.ext} &&
+        meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_maternal_${i}.${read.ext} output 'maternal${i}.meryl' &&
+    #end for
+    meryl union-sum maternal*.meryl output mat.meryl &&
+    #for $i, $read in enumerate($child_reads):
+        mkdir 'child${i}.meryl' &&
+        ln -s '$read' ./input_child_${i}.${read.ext} &&
+        meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
+    #end for
+    meryl union-sum child*.meryl output child.meryl &&
+    meryl histogram child.meryl > read-db.hist &&                                          
+    tar -czf 'read-db.meryldb' child.meryl &&
+    
+    ## mat specific kmers
+    meryl difference mat.meryl pat.meryl output mat.only.meryl &&
+    meryl histogram mat.only.meryl > mat.only.hist &&
+    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy &&
+    VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` &&
+    meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl &&
+
+    ## pat specific kmers
+    meryl difference pat.meryl mat.meryl output pat.only.meryl &&
+    meryl histogram pat.only.meryl > pat.only.hist &&
+    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy &&
+    VAR=`sed -n 2p pat.only.ploidy | awk '{print \$NF}'` &&
+    meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl &&
+
+    ## shared kmers
+    meryl intersect output shared.meryl mat.meryl pat.meryl &&
+
+    ## mat hapmers
+    meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl &&
+    meryl histogram mat.inherited.meryl > mat.inherited.hist &&
+    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy &&
+    VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` &&
+    meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl &&
+    tar -czf 'mat.meryldb' mat.hapmer.meryl &&
+
+    ## pat hapmers
+    meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl &&
+    meryl histogram pat.inherited.meryl > pat.inherited.hist &&
+    java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
+    VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` &&
+    meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
+    tar -czf 'pat.meryldb' pat.hapmer.meryl &&
+
+    echo 'K-mer size: ${size}'
+    ]]></command>
+    <inputs>
+        <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly"/>
+        <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly"/>
+        <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly"/>
+        <conditional name="options_kmer_size">
+            <param name="kmer_size" type="select" label="K-mer size selector">
+                <option value="provide">Set a k-mer size</option>
+                <option value="estimate">Estimate the best k-mer size</option>
+            </param>
+            <when value="provide">
+                <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G)."/>
+            </when>
+            <when value="estimate">
+                <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
+                <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"/>
+        <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"/>
+        <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb"/>
+        <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram"/>
+        <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb"/>
+        <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="6">
+            <conditional name="options_kmer_size">
+                <param name="kmer_size" value="provide"/>
+                <param name="input_kmer_size" value="21"/>
+            </conditional>
+            <param name="maternal_reads" value="maternal.fasta"/>
+            <param name="paternal_reads" value="paternal.fasta"/>
+            <param name="child_reads" value="child.fasta"/>
+            <output name="read_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="3362942" delta="2000"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+            <output name="read_db_hist" file="output_23.read-db.hist"/>
+            <output name="pat_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="120610" delta="400"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+            <output name="pat_db_hist" file="output_23.pat.hist"/>
+            <output name="mat_db" ftype="meryldb">
+                <assert_contents>
+                    <has_size value="67883" delta="300"/>
+                    <expand macro="meryldb_archive_assumptions"/>
+                </assert_contents>
+            </output>
+            <output name="mat_db_hist" file="output_23.mat.hist"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**Purpose**
+
+Meryl is the k-mer counter. This tool builds hap-mer databases  for trios, in accordance
+with `merqury's recommended guidelines. &lt;https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios&gt;`_
+
+        </help>
+    <expand macro="citations"/>
+</tool>