# HG changeset patch
# User bioitcore
# Date 1504817592 14400
# Node ID cd336e593a92a745f01ea92bab808ee4dd21fa25
# Parent  312539ee12f4b5b929c5c1855ce1bfb23df04935
planemo upload

diff -r 312539ee12f4 -r cd336e593a92 splice_trap.xml
--- a/splice_trap.xml	Thu Sep 07 15:29:43 2017 -0400
+++ b/splice_trap.xml	Thu Sep 07 16:53:12 2017 -0400
@@ -4,17 +4,35 @@
     <requirements>
         <requirement type="package" version="1.2.1.1">bowtie</requirement>
     </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        perl $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 "$input1" -2 "$input2" -s "$read_size" "$output1" "$output2"
-    ]]></command>
+    <command detect_errors="exit_code" interpreter="perl">
+    $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 
+    #if $input_type_conditional.spliceTrap_input_type == "paired"
+            $input_type_conditional.input_1 -2 $input_type_conditional.input_2
+    #else
+            $input_type_conditional.input.forward -2 $input_type_conditional.input.reverse
+    #end if 
+    -s $read_size $output1 $output2
+    </command>
     <inputs>
-        <param type="data" name="input1" format="fastq" />
-        <param type="data" name="input2" format="fastq" />
-        <param name='read_size' type='integer' value='50' label="Read size"  />
+            <conditional name="input_type_conditional">
+                    <param name="spliceTrap_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
+                            <option value="paired" selected="true">Paired</option>
+                            <option value="paired_collection">Paired Collection</option>
+                    </param>
+                    <when value="paired">
+                            <param format='fastq' name='input_1' type='data' label="FASTQ file, reverse reads" />
+                            <param format='fastq' name='input_2' type='data' label="FASTQ file, forward reads" />
+                    </when>
+                    <when value="paired_collection">
+                            <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
+                    </when>
+            </conditional>
+            
+            <param name='read_size' type='integer' value='50' label="Read size"  />
     </inputs>
     <outputs>
-        <data name="output1" format="txt" />
-        <data name="output2" format="txt" />
+            <data format="txt" name="output1" />
+            <data format="txt" name="output2" />
     </outputs>
     <tests>
         <test>
@@ -24,7 +42,7 @@
             <output name="output2" file="output2.txt"/>
         </test>
     </tests>
-    <help> 
+    <help>
         **SpliceTrap**
     </help>
     <citations>
@@ -33,3 +51,4 @@
         </citation>
     </citations>
 </tool>
+