# HG changeset patch
# User sanbi-uwc
# Date 1484937317 18000
# Node ID 5c5a2a7e9cbbd92b948eab2abeb1c82807b089c4
# Parent  bbe75c52b3005764a6aedcbb64cc68e4a3e27b17
planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 213668d2e5a61c806ad992c201ae6e304c6e0965

diff -r bbe75c52b300 -r 5c5a2a7e9cbb trimmomatic.xml
--- a/trimmomatic.xml	Fri Jan 20 08:57:21 2017 -0500
+++ b/trimmomatic.xml	Fri Jan 20 13:35:17 2017 -0500
@@ -4,24 +4,21 @@
     <requirement type="package" version="0.36">trimmomatic</requirement>
   </requirements>
   <command detect_errors="aggressive"><![CDATA[
-  #if $paired_end.is_paired_end
-    #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
-    #if $paired_input_type == "pair_of_files"
-      #set r1_ext = $paired_end.paired_input_type_conditional.fastq_r1_in.extension
-      #set r2_ext = $paired_end.paired_input_type_conditional.fastq_r2_in.extension
-      ln -s '${paired_end.paired_input_type_conditional.fastq_r1_in}' fastq_r1.'$r1_ext' &&
-      ln -s '${paired_end.paired_input_type_conditional.fastq_r2_in}' fastq_r2.'$r2_ext' &&
-    #else
-      #set r1_ext = $paired_end.paired_input_type_conditional.fastq_pair.forward.extension
-      #set r2_ext = $paired_end.paired_input_type_conditional.fastq_pair.reverse.extension
-      ln -s '${paired_end.paired_input_type_conditional.fastq_pair.forward}' fastq_r1.'$r1_ext' &&
-      ln -s '${paired_end.paired_input_type_conditional.fastq_pair.reverse}' fastq_r2.'$r2_ext' &&
-    #end if
+  #if $readtype.single_or_paired == "pair_of_files"
+    #set r1_ext = $readtype.fastq_r1_in.extension
+    #set r2_ext = $readtype.fastq_r2_in.extension
+    ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' &&
+    ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' &&
+  #elif $readtype.single_or_paired == "collection"
+    #set r1_ext = $readtype.fastq_pair.forward.extension
+    #set r2_ext = $readtype.fastq_pair.reverse.extension
+    ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' &&
+    ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' &&
   #else
-      ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
+    ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
   #end if
   bash '${__tool_directory__}/trimmomatic.sh'
-  #if $paired_end.is_paired_end
+  #if $readtype.single_or_paired in ["pair_of_files","collection"]
     PE -threads \${GALAXY_SLOTS:-6} -phred33
       fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
       fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
@@ -63,59 +60,50 @@
     #end if
   #end for
   &&
-  #if $paired_end.is_paired_end
-    #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
-    #if $paired_input_type == "pair_of_files"
-      mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
-      mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
-      mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
-      mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
-    #else
-      mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
-      mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
-      mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
-      mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
-    #end if
+  #if $readtype.single_or_paired  == "pair_of_files"
+    mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
+    mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
+    mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
+    mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
+  #elif $readtype.single_or_paired  == "collection"
+    mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
+    mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
+    mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
+    mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
   #else
     mv fastq_out.'$fastq_in.extension' '${fastq_out}'
   #end if
   ]]></command>
   <inputs>
-    <conditional name="paired_end">
-    <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="True" />
-    <when value="no">
-      <param name="fastq_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file" />
-    </when>
-    <when value="yes">
-      <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>
+    <conditional name="readtype">
+        <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
+           <option value="se" selected="true">Single-end</option>
+           <option value="pair_of_files">Paired-end (two separate input files)</option>
+           <option value="collection">Paired-end (as collection)</option>
         </param>
-        <when value="pair_of_files">
- 	  <param name="fastq_r1_in" type="data" format="fastqsanger|fastqsanger.gz"
-		 label="Input FASTQ file (R1/first of pair)" />
- 	  <param name="fastq_r2_in" type="data" format="fastqsanger|fastqgsanger.gz"
-		 label="Input FASTQ file (R2/second of pair)" />
-	</when>
+    <when value="se">
+      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
+    </when>
+    <when value="pair_of_files">
+      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz"
+         label="Input FASTQ file (R1/first of pair)" />
+      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqgsanger.gz"
+         label="Input FASTQ file (R2/second of pair)" />
+    </when>
         <when value="collection">
-          <param name="fastq_pair" format="fastqsanger|fastqsanger.gz" type="data_collection"
- 		 collection_type="paired"
- 		 label="Select FASTQ dataset collection with R1/R2 pair" />
+          <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
         </when>
       </conditional>
-    </when>
-    </conditional>
     <conditional name="illuminaclip">
     <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="False" />
     <when value="yes">
       <param name="adapter_fasta" type="select" label="Adapter sequences to use">
-	<option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
-	<option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
-	<option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
-	<option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
-	<option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
-	<option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
+    <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
+    <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
+    <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
+    <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
+    <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
+    <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
       </param>
       <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
       <param name="palindrome_clip_threshold" type="integer" label="How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment" value="30" />
@@ -125,91 +113,77 @@
     </conditional>
     <repeat name="operations" title="Trimmomatic Operation" min="1">
       <conditional name="operation">
-	<param name="name" type="select" label="Select Trimmomatic operation to perform">
-	  <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
-	  <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
-	  <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
-	  <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
-	  <option value="CROP">Cut the read to a specified length (CROP)</option>
-	  <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
-	  <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
-	  <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
-	</param>
-	<when value="SLIDINGWINDOW">
-	  <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
-	  <param name="required_quality" type="integer" label="Average quality required" value="20" />
-	</when>
-	<when value="MINLEN">
-	  <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
-	</when>
-	<when value="LEADING">
-	  <param name="leading" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the start of the read with quality below the threshold will be removed" />
-	</when>
-	<when value="TRAILING">
-	  <param name="trailing" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the end of the read with quality below the threshold will be removed" />
-	</when>
-	<when value="CROP">
-	  <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
-	</when>
-	<when value="HEADCROP">
-	  <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
-	</when>
-	<when value="AVGQUAL">
-	  <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
-	</when>
-	<when value="MAXINFO">
-	  <param name="target_length" type="integer" label="Target read length" value="" help="The read length which is likely to allow the location of the read within the target sequence to be determined." />
-	  <param name="strictness" type="float" label="Strictness" value="" help="Set between zero and one - specifies the balance between preserving read length versus removal of incorrect bases; low values (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
-	</when>
+    <param name="name" type="select" label="Select Trimmomatic operation to perform">
+      <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
+      <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
+      <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
+      <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
+      <option value="CROP">Cut the read to a specified length (CROP)</option>
+      <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
+      <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
+      <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
+    </param>
+    <when value="SLIDINGWINDOW">
+      <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
+      <param name="required_quality" type="integer" label="Average quality required" value="20" />
+    </when>
+    <when value="MINLEN">
+      <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
+    </when>
+    <when value="LEADING">
+      <param name="leading" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the start of the read with quality below the threshold will be removed" />
+    </when>
+    <when value="TRAILING">
+      <param name="trailing" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the end of the read with quality below the threshold will be removed" />
+    </when>
+    <when value="CROP">
+      <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
+    </when>
+    <when value="HEADCROP">
+      <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
+    </when>
+    <when value="AVGQUAL">
+      <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
+    </when>
+    <when value="MAXINFO">
+      <param name="target_length" type="integer" label="Target read length" value="" help="The read length which is likely to allow the location of the read within the target sequence to be determined." />
+      <param name="strictness" type="float" label="Strictness" value="" help="Set between zero and one - specifies the balance between preserving read length versus removal of incorrect bases; low values (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
+    </when>
       </conditional>
     </repeat>
   </inputs>
   <outputs>
-    <data name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)"
-      format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}">
-      <filter>paired_end['is_paired_end']</filter>
-      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
+      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)"
-      format_source="${paired_end.paired_input_type_conditional.fastq_r2_in}">
-      <filter>paired_end['is_paired_end']</filter>
-      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
+      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)"
-      format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}">
-      <filter>paired_end['is_paired_end']</filter>
-      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
+      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)"
-      format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}">
-      <filter>paired_end['is_paired_end']</filter>
-      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
+      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}"
-      format_source="${fastq_in}">
-      <filter>not paired_end['is_paired_end']</filter>
+    <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
+      <filter>readtype['single_or_paired'] == 'se'</filter>
     </data>
-    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired">
-      <data name="forward" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)"
-        format_source="${paired_end.paired_input_type_conditional.fastq_pair.forward}" />
-      <data name="reverse" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)"
-        format_source="${paired_end.paired_input_type_conditional.fastq_pair.reverse}" />
-      <filter>paired_end['is_paired_end']</filter>
-      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
+    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired">
+      <filter>readtype['single_or_paired'] == "collection"</filter>
+      <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
+      <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
     </collection>
-    <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired">
-      <data name="forward" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)"
-        format_source="${paired_end.paired_input_type_conditional.fastq_pair.forward}" />
-      <data name="reverse" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)"
-        format_source="${paired_end.paired_input_type_conditional.fastq_pair.reverse}" />
-      <filter>paired_end['is_paired_end']</filter>
-      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
+      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired">
+        <filter>readtype['single_or_paired'] == "collection"</filter>
+        <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
+        <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
     </collection>
+
   </outputs>
   <tests>
     <test>
       <!-- Single-end example -->
-      <param name="is_paired_end" value="no" />
+      <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
       <!--
@@ -221,7 +195,7 @@
     </test>
     <test>
       <!-- Single-end example - gzipped -->
-      <param name="is_paired_end" value="no" />
+      <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
       <!--
@@ -233,7 +207,7 @@
     </test>
     <test>
       <!-- Paired-end example - gzipped -->
-      <param name="is_paired_end" value="yes" />
+      <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
       <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
@@ -249,7 +223,7 @@
     </test>
     <test>
       <!-- Paired-end example -->
-      <param name="is_paired_end" value="yes" />
+      <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
@@ -265,7 +239,7 @@
     </test>
     <test>
       <!-- Single-end example (cropping) -->
-      <param name="is_paired_end" value="no" />
+      <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="operations_0|operation|name" value="CROP" />
       <param name="operations_0|operation|crop" value="10" />
@@ -278,8 +252,7 @@
     </test>
     <test>
       <!-- Paired-end with dataset collection -->
-      <param name="is_paired_end" value="yes" />
-      <param name="paired_input_type" value="collection" />
+      <param name="single_or_paired" value="collection" />
       <param name="fastq_pair">
         <collection type="paired">
           <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -298,8 +271,7 @@
     </test>
     <test>
       <!-- Paired-end with dataset collection - gzipped -->
-      <param name="is_paired_end" value="yes" />
-      <param name="paired_input_type" value="collection" />
+      <param name="single_or_paired" value="collection" />
       <param name="fastq_pair">
         <collection type="paired">
           <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
@@ -318,7 +290,7 @@
     </test>
     <test>
       <!-- Single-end using AVGQUAL -->
-      <param name="is_paired_end" value="no" />
+      <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="operations_0|operation|name" value="AVGQUAL" />
       <param name="operations_0|operation|avgqual" value="30" />
@@ -326,7 +298,7 @@
     </test>
     <test>
       <!-- Single-end using MAXINFO -->
-      <param name="is_paired_end" value="no" />
+      <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="operations_0|operation|name" value="MAXINFO" />
       <param name="operations_0|operation|target_length" value="75" />