FastK: Added ktab files to output and minor changes (galaxyproject#6007)

* Added ktab files to output and minor changes * version bump
bebatut · May 14, 2024 · dbdc7c7 · dbdc7c7
1 parent 8dc7b89
commit dbdc7c7
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Showing 2 changed files with 18 additions and 11 deletions.
diff --git a/tools/fastk/fastk.xml b/tools/fastk/fastk.xml
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir -p outfiles/tmpfiles && 
+        mkdir -p outfiles/ktabfiles && 
         #if $infile.is_of_type("fastq"):
             #set INPUTFILE="input.fastq"
         #elif $infile.is_of_type("fastq.gz"):
@@ -21,17 +21,21 @@
         #elif $sorted_table.sorted_table_option == 'yes_with_custom':
             -t$sorted_table_cutoff 
         #end if
-        -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/tmpfiles
+        -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/ktabfiles
         #if $sorted_table.sorted_table_option == 'yes_with_default':
             && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist'
+            && mv outfiles/.*.ktab* outfiles/ktabfiles 
+            && mv outfiles/*.ktab outfiles/ktabfiles
         #elif $sorted_table.sorted_table_option == 'yes_with_custom':
             && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist'
+            && mv outfiles/.*.ktab* outfiles/ktabfiles 
+            && mv outfiles/*.ktab outfiles/ktabfiles
         #end if
         && tar -c -f fastk.tar ./outfiles/
     ]]></command>
     <inputs>
         <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/>   
-        <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40" />
+        <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40"/>
         <conditional name="sorted_table">
             <param name="sorted_table_option" type="select" label="Sort table" help="Do you want a sorted table of all canonical k-mers and their counts? The sorted table is sorted lexicographically on the k-mer where a &lt; c &lt; g &lt; t.">
                 <option value="no">No</option>
@@ -50,7 +54,10 @@
     </inputs>
     <outputs>
         <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${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 ${on_string}: FastK hist" />
+        <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist"/>
+        <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="outfiles/ktabfiles/output.ktab" label="${tool.name} on ${on_string}: FastK ktab">
+            <filter> sorted_table['sorted_table_option'] != 'no' </filter> 
+        </data>
         <data name="tabex_hist" format="txt"  label="${tool.name} on ${on_string}: Tabex output">
             <filter> sorted_table['sorted_table_option'] != 'no' </filter>
         </data>
@@ -66,21 +73,21 @@
             </output>
         </test>
         <!-- TEST 2 -->
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <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"/>
+                    <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
                 </assert_contents>
             </output>
-            <output name="tabex_hist" value="test02.tabex.txt"/>
+            <output name="tabex_hist" file="test02.tabex.txt"/>
         </test>
         <!-- TEST 3 -->
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <param name="infile" value="input01.fasta.gz"/>
             <conditional name="sorted_table">
                 <param name="sorted_table_option" value="yes_with_custom"/>
@@ -89,10 +96,10 @@
             <output name="fastk_out" ftype="tar">
                 <assert_contents>
                     <has_archive_member path="./outfiles/output.hist"/>
-                    <has_archive_member path="./outfiles/output.ktab"/>
+                    <has_archive_member path="./outfiles/ktabfiles/output.ktab"/>
                 </assert_contents>
             </output>
-            <output name="tabex_hist" value="test03.tabex.txt"/>
+            <output name="tabex_hist" file="test03.tabex.txt"/>
         </test>       
     </tests>
     <help><![CDATA[

diff --git a/tools/fastk/macros.xml b/tools/fastk/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">fastk</requirement>