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diff trimmomatic.xml @ 3:f8a9a5eaca8a draft

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Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
author pjbriggs
date Wed, 23 Sep 2015 08:59:23 -0400
parents a60283899c6d
children 14d05f2d511d
line wrap: on
line diff
--- a/trimmomatic.xml	Wed Apr 22 09:36:27 2015 -0400
+++ b/trimmomatic.xml	Wed Sep 23 08:59:23 2015 -0400
@@ -1,12 +1,31 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.32.2">
+<tool id="trimmomatic" name="Trimmomatic" version="0.32.3">
   <description>flexible read trimming tool for Illumina NGS data</description>
-  <command interpreter="bash">trimmomatic.sh
+  <requirements>
+    <requirement type="package" version="0.32">trimmomatic</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command interpreter="bash"><![CDATA[
+  trimmomatic.sh
   -mx8G
   -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
   #if $paired_end.is_paired_end
-    PE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired 
+    PE -threads \${GALAXY_SLOTS:-6} -phred33
+    #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
+    #if $paired_input_type == "pair_of_files"
+      "${paired_end.paired_input_type_conditional.fastq_r1_in}"
+      "${paired_end.paired_input_type_conditional.fastq_r2_in}"
+      "${fastq_out_r1_paired}" "${fastq_out_r1_unpaired}"
+      "${fastq_out_r2_paired}" "${fastq_out_r2_unpaired}"
+    #else
+      "${paired_end.paired_input_type_conditional.fastq_pair.forward}"
+      "${paired_end.paired_input_type_conditional.fastq_pair.reverse}"
+      "${fastq_out_paired.forward}" "${fastq_out_unpaired.forward}"
+      "${fastq_out_paired.reverse}" "${fastq_out_unpaired.reverse}"
+    #end if
   #else
-    SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out
+    SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out"
   #end if
   ## ILLUMINACLIP option
   #if $illuminaclip.do_illuminaclip
@@ -35,10 +54,7 @@
       HEADCROP:$op.operation.headcrop
     #end if
   #end for
-  </command>
-  <requirements>
-    <requirement type="package" version="0.32">trimmomatic</requirement>
-  </requirements>
+  ]]></command>
   <inputs>
     <conditional name="paired_end">
     <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
@@ -46,10 +62,23 @@
       <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />
     </when>
     <when value="yes">
-      <param name="fastq_r1_in" type="data" format="fastqsanger"
-	     label="Input FASTQ file (R1/first of pair)" />
-      <param name="fastq_r2_in" type="data" format="fastqsanger"
-	     label="Input FASTQ file (R2/second of pair)" />
+      <conditional name="paired_input_type_conditional">
+        <param name="paired_input_type" type="select" label="Input Type">
+          <option value="pair_of_files" selected="true">Pair of datasets</option>
+          <option value="collection">Dataset collection pair</option>
+        </param>
+        <when value="pair_of_files">
+ 	  <param name="fastq_r1_in" type="data" format="fastqsanger"
+		 label="Input FASTQ file (R1/first of pair)" />
+ 	  <param name="fastq_r2_in" type="data" format="fastqsanger"
+		 label="Input FASTQ file (R2/second of pair)" />
+	</when>
+        <when value="collection">
+          <param name="fastq_pair" format="fastqsanger" type="data_collection"
+ 		 collection_type="paired"
+ 		 label="Select FASTQ dataset collection with R1/R2 pair" />
+        </when>
+      </conditional>
     </when>
     </conditional>
     <conditional name="illuminaclip">
@@ -101,21 +130,37 @@
     </repeat>
   </inputs>
   <outputs>
-    <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${on_string} (R1 paired)">
+    <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)">
       <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
     </data>
-    <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${on_string} (R1 unpaired)">
+    <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)">
       <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
     </data>
-    <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${on_string} (R2 paired)">
+    <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)">
       <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
     </data>
-    <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${on_string} (R2 unpaired)">
+    <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)">
       <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
     </data>
-    <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${on_string}">
+    <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}">
       <filter>not paired_end['is_paired_end']</filter>
     </data>
+    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired">
+      <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" />
+      <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" />
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
+    </collection>
+    <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired">
+      <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" />
+      <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" />
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
+    </collection>
   </outputs>
   <tests>
     <test>
@@ -159,8 +204,28 @@
       -->
       <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
     </test>
+    <test>
+      <!-- Paired-end with dataset collection -->
+      <param name="is_paired_end" value="yes" />
+      <param name="paired_input_type" value="collection" />
+      <param name="fastq_pair">
+        <collection type="paired">
+          <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+          <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
+        </collection>
+      </param>
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output_collection name="fastq_out_paired" type="paired">
+	<element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
+	<element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
+      </output_collection>
+      <output_collection name="fastq_out_unpaired" type="paired">
+	<element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
+	<element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
+      </output_collection>
+    </test>
   </tests>
-  <help>
+  <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -191,6 +256,14 @@
 
 .. class:: infomark
 
+**Inputs**
+
+For single-end data this Trimmomatic tool accepts a single FASTQ file; for
+paired-end data it will accept either two FASTQ files (R1 and R2), or a
+dataset collection containing the R1/R2 FASTQ pair.
+
+.. class:: infomark
+
 **Outputs**
 
 For paired-end data a particular strength of Trimmomatic is that it retains the
@@ -201,6 +274,12 @@
  * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
    one of the pair failed the filtering steps.
 
+.. class:: warningmark
+
+If the input consists of a dataset collection with the R1/R2 FASTQ pair then
+the outputs will also inclue two dataset collections: one for the 'paired'
+outputs and one for the 'unpaired' (as described above)
+
 Retaining the same order and number of reads in the filtered output fastq files is
 essential for many downstream analysis tools.
 
@@ -228,7 +307,7 @@
 
 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
 use it.
-  </help>
+  ]]></help>
   <citations>
     <!--
     See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set