# HG changeset patch
# User yhoogstrate
# Date 1424418556 18000
# Node ID dd2ec1b37e9692889dc7e3e0e56fbc83f3948f38
# Parent  c6a790326d1eda4158bd6e585116631a532b60a8
Added support for the "pair"-data collection type.

diff -r c6a790326d1e -r dd2ec1b37e96 sickle.xml
--- a/sickle.xml	Mon Jul 15 12:12:41 2013 -0500
+++ b/sickle.xml	Fri Feb 20 02:49:16 2015 -0500
@@ -4,50 +4,68 @@
 		<requirement type="package" version="1.21.0">sickle</requirement>
 	</requirements>
 	<command>
-		sickle $readtype.single_or_paired --quiet
-
+		sickle
+		
 		#if str($readtype.single_or_paired) == "se":
-		-f $input_single -t $qual_type -o $output_single
+			 se
+		#else
+			 pe
 		#end if
-
+		
+		 --quiet
+		
+		#if str($readtype.single_or_paired) == "se":
+			 -f $input_single -t $qual_type -o $output_single
+		#end if
+		
 		#if str($readtype.single_or_paired) == "pe":
-		-f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
+			 -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
 		#end if
-
+		
+		#if str($readtype.single_or_paired) == "pe_collection":
+			 -f "$readtype.input_paired.forward" -r "$readtype.input_paired.reverse" -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
+		#end if
+		
 		#if str($qual_threshold) != "":
-		-q $qual_threshold
+			-q $qual_threshold
 		#end if
-
+		
 		#if str($length_threshold) != "":
-		-l $length_threshold
+			 -l $length_threshold
 		#end if
 
 		#if $no_five_prime:
-		-x
+				 -x
 		#end if
 
 		#if $discard_n:
 		-n
 		#end if
 	</command>
-
+	
 	<inputs>
+		<!-- original wrapper code -->
 		<conditional name="readtype">
 			<param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?">
 				<option value="se" selected="true">Single-End</option>
 				<option value="pe">Paired-End</option>
+				<option value="pe_collection">Paired-End (as collection)</option>
 			</param>
-
+			
 			<when value="se">
 				<param format="fastq, fastqsanger" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/>
 			</when>
-
+			
 			<when value="pe">
 				<param format="fastq, fastqsanger" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/>
 				<param format="fastq, fastqsanger" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/>
 			</when>
+			
+			<when value="pe_collection">
+				<param format="fastq, fastqsanger" name="input_paired" type="data_collection" collection_type="paired" optional="false" label="Paired-End FastQ Reads as paired collection" />
+			</when>
 		</conditional>
-
+		
 		<param name="qual_type" type="select" optional="false" label="Quality type">
 			<option value="illumina" selected="true">Illumina</option>
 			<option value="solexa">Solexa</option>
@@ -72,15 +90,15 @@
 		</data>
 
 		<data format_source="input_paired1" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}">
-		<filter>(readtype['single_or_paired'] == 'pe')</filter>
+		<filter>(readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')</filter>
 		</data>
 
 		<data format_source="input_paired2" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}">
-		<filter>(readtype['single_or_paired'] == 'pe')</filter>
+		<filter>(readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')</filter>
 		</data>
 
 		<data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}">
-		<filter>(readtype['single_or_paired'] == 'pe')</filter>
+		<filter>(readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')</filter>
 		</data>
 	</outputs>
 	<tests>