Updated FASTK tool wrapper

tools/fastk/.shed.yml

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+name: fastk
+owner: iuc
+categories:
+- Assembly
+description: "FastK: A K-mer counter (for HQ assembly data sets)"
+long_description: FastK is a k‑mer counter that is optimized for processing high-quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
+homepage_url: https://github.com/thegenemyers/FASTK
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk
+type: unrestricted
+suite:
+  name: "suite_fastk"
+  description: "A suite of tools for FASTK in Galaxy"
+  type: repository_suite_definition
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the FASTK tool suite: {{ tool_name }}"

tools/fastk/fastk.xml

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+<tool id="fastk_fastk" name="FastK" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
+    <description>A k-mer counter for high-quality assembly datasets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p outfiles/tmpfiles && 
+        #if $infile.is_of_type("fastq"):
+            #set INPUTFILE="input.fastq"
+        #elif $infile.is_of_type("fastq.gz"):
+            #set INPUTFILE="input.fastq.gz"
+        #else
+            #set INPUTFILE="input."+$infile.ext
+        #end if
+        ln -s '$infile' $INPUTFILE && 
+        FastK $INPUTFILE 
+        -k$kmer_size 
+        #if $sorted_table.sorted_table_option == 'yes_with_default':
+            -t 
+        #elif $sorted_table.sorted_table_option == 'yes_with_custom':
+            -t$sorted_table_cutoff 
+        #end if
+        -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/tmpfiles
+        #if $sorted_table.sorted_table_option == 'yes_with_default':
+            && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
+        #elif $sorted_table.sorted_table_option == 'yes_with_custom':
+            && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
+        #end if
+        && tar -c -f fastk.tar ./outfiles/
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>   
+        <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40" />
+        <conditional name="sorted_table">
+            <param name="sorted_table_option" type="select" label="Sort table" help="Do you want a sorted table of all canonical k-mers and their counts? The sorted table is sorted lexicographically on the k-mer where a &lt; c &lt; g &lt; t.">
+                <option value="no">No</option>
+                <option value="yes_with_default">Yes, Default sorted </option>
+                <option value="yes_with_custom">Yes, Custom sorted </option>
+            </param>
+            <when value="no"/>
+            <when value="yes_with_default">
+                <param name="tabex_threshold_for_default" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/>
+            </when>
+            <when value="yes_with_custom">
+                <param name="sorted_table_cutoff" type="integer" min="2" value="10" label="Enter sorted table cutoff value"/>
+                <param name="tabex_threshold_for_custom" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/>
+        <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist" />
+        <data name="tabex_hist" format="txt"  label="${tool.name} on ${on_string}: Tabex output">
+            <filter> sorted_table['sorted_table_option'] != 'no' </filter>
+        </data>
+    </outputs>
+    <tests>
+    <!-- TEST 1 -->
+        <test expect_num_outputs="2">
+            <param name="infile" value="input01.fasta.gz"/>
+            <output name="fastk_out" ftype="tar">
+                <assert_contents>
+                    <has_archive_member path="./outfiles/output.hist"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- TEST 2 -->
+        <test expect_num_outputs="3">
+            <param name="infile" value="input01.fasta.gz"/>
+            <conditional name="sorted_table">
+                <param name="sorted_table_option" value="yes_with_default"/>
+            </conditional>
+            <output name="fastk_out" ftype="tar">
+                <assert_contents>
+                    <has_archive_member path="./outfiles/output.hist"/>
+                    <has_archive_member path="./outfiles/output.ktab"/>
+                </assert_contents>
+            </output>
+            <output name="tabex_hist" value="test02.tabex.txt"/>
+        </test>
+        <!-- TEST 3 -->
+        <test expect_num_outputs="3">
+            <param name="infile" value="input01.fasta.gz"/>
+            <conditional name="sorted_table">
+                <param name="sorted_table_option" value="yes_with_custom"/>
+                <param name="sorted_table_cutoff" value="5"/>
+            </conditional>
+            <output name="fastk_out" ftype="tar">
+                <assert_contents>
+                    <has_archive_member path="./outfiles/output.hist"/>
+                    <has_archive_member path="./outfiles/output.ktab"/>
+                </assert_contents>
+            </output>
+            <output name="tabex_hist" value="test03.tabex.txt"/>
+        </test>       
+    </tests>
+    <help><![CDATA[
+        FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
+
+        The input data can be in CRAM, BAM, SAM, fasta, or fastq files.
+
+        FastK produces the following outputs:
+
+        1. A .hist file in binary format containing histogram information detailing the frequency of occurrence for each k‑mer within the dataset.
+
+        2. A Tabex txt file comprising a table of k‑mer/count pairs, sorted lexicographically on the k‑mer sequence, followingthe order a < c < g < t
+
+        3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools.
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

tools/fastk/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">fastk</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">                                                                   
+                @misc{github,                                                                 
+                author = {Gene Meyers},
+                year = {2020},                                                                 
+                title = {FastK},                                                        
+                publisher = {GitHub},
+                journal = {GitHub repository},                                               
+                url = {https://github.com/thegenemyers/FASTK},                        
+                }                                                                    
+            </citation>
+        </citations>
+    </xml>
+</macros>