# HG changeset patch
# User bioitcore
# Date 1504820364 14400
# Node ID 2ebca9da5e4236b42bbde87fd3170809a7efbcee
# Parent  cd336e593a92a745f01ea92bab808ee4dd21fa25
planemo upload

diff -r cd336e593a92 -r 2ebca9da5e42 splice_trap.xml
--- a/splice_trap.xml	Thu Sep 07 16:53:12 2017 -0400
+++ b/splice_trap.xml	Thu Sep 07 17:39:24 2017 -0400
@@ -14,21 +14,21 @@
     -s $read_size $output1 $output2
     </command>
     <inputs>
-            <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"  />
+        <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 format="txt" name="output1" />
@@ -41,6 +41,17 @@
             <output name="output1" file="output1.txt"/>
             <output name="output2" file="output2.txt"/>
         </test>
+        <test>
+            <param name="fastq_input">
+              <collection type="paired">
+                <element name="forward" value="input1.fastq" />
+                <element name="reverse" value="input2.fastq" />
+              </collection>
+            </param>
+            <param name="input_type" value="paired_collection" />
+            <output name="output1" file="output1.txt"/>
+            <output name="output2" file="output2.txt"/>
+        </test>
     </tests>
     <help>
         **SpliceTrap**