# HG changeset patch
# User simon-gladman
# Date 1405013093 14400
# Node ID 76d1aebc44bfaacd4dea1c1f6f0865fd9c95cc67
# Parent  9db0c1c78236269106fb6214ceb06c7359fd2517
Uploaded: added dataset collection support for paired end trimmomatic

diff -r 9db0c1c78236 -r 76d1aebc44bf trimmomatic.xml
--- a/trimmomatic.xml	Thu Jul 10 12:21:33 2014 -0400
+++ b/trimmomatic.xml	Thu Jul 10 13:24:53 2014 -0400
@@ -8,10 +8,16 @@
     <command interpreter="perl">
         trimmomatic_wrapper.pl
             paired ${paired.is_paired}
-            fwdfile ${paired.forwards_file}
-            #if $paired.is_paired:
+            #if $paired.is_paired == "single":
+                fwdfile ${paired.forwards_file}
+            #end if
+            #if $paired.is_paired == "paired":
+                fwdfile ${paired.forwards_file}
                 revfile ${paired.reverse_file}
             #end if
+            #if $paired.is_paired == "collection":
+                fwdfile ${collection_data.forward}
+                revfile ${collection_data.reverse}
             phred $phred
             cutadapt ${adapt.adapters}
             #if $adapt.adapters:
@@ -59,7 +65,12 @@
     <inputs>
         
         <conditional name="paired">
-            <param name="is_paired" type="boolean" checked="true" truevalue="paired" falsevalue="single" label="Paired end reads?" help="Do you have 2 separate paired end read files?"/>
+<!--            <param name="is_paired" type="boolean" checked="true" truevalue="paired" falsevalue="single" label="Paired end reads?" help="Do you have 2 separate paired end read files?"/> -->
+            <param name="is_paired" type="select" label="Read type selector" help="single file (not pair aware), two files (paired reads) or a dataset collection of pairs">
+                <option value="single" selected="true">Single File</option>
+                <option value="paired">Two Files</option>
+                <option value="collection">Single dataset collection pair</option>
+            </param>
             <when value="paired">
                 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 1 fastq reads to trim"/>
                 <param name="reverse_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 2 fastq reads to trim"/>
@@ -67,6 +78,9 @@
             <when value="single">
                 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Fastq reads to trim"/>
             </when>
+            <when value="collection">
+                <param name="collection_data" type="data_collection" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Paired end dataset collection" collection_type="paired"/>
+            </when>
         </conditional>
         <param name="phred" type="select" label="Quality encoding." help="Phred33 or Phred 64, probably Phred64">
             <option value="phred64">phred64</option>
@@ -140,10 +154,10 @@
         <data name="log" format="tabular" label="${tool.name} on ${on_string}: Trimmomatic Log" hidden="True">
         </data>
         <data name="fwdpairs" format="input" label="${tool.name} on ${on_string}: Dir1 trimmed pairs">
-            <filter>(paired['is_paired'])</filter>
+            <filter>(paired['is_paired']=="single")</filter>
         </data>
         <data name="revpairs" format="input" label="${tool.name} on ${on_string}: Dir2 trimmed pairs">
-            <filter>(paired['is_paired'])</filter>
+            <filter>(paired['is_paired'] == "paired" or paired['is_paired'] == "collection")</filter>
         </data>
         <data name="singles" format="input" label="${tool.name} on ${on_string}: trimmed reads"/>
         <data name="dummy_out" format="tabular" label="${tool.name} on ${on_string}: DEBUG OUTPUT" hidden="True"/>