Mercurial > repos > estrain > sum_fastqc

changeset 2:226ce8aaa97a draft

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Uploaded
author estrain
date Tue, 16 Oct 2018 18:59:44 -0400
parents 52c14941b49f
children 5e1f199bd289
files sum_fastqc.xml
diffstat 1 files changed, 7 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/sum_fastqc.xml	Tue Oct 16 17:16:03 2018 -0400
+++ b/sum_fastqc.xml	Tue Oct 16 18:59:44 2018 -0400
@@ -4,14 +4,14 @@
     <command detect_errors="exit_code"><![CDATA[
 
       #if $jobtype.select == "single"
-        #set inname = $jobtype.single.name
-        #set infile = $jobtype.single
+        #set inname = $jobtype.file.name
+        #set infile = $jobtype.file
       #else if $jobtype.select == "col"
-        #set inname = $jobtype.col.name
-        #set infile = $jobtype.col.coll
+        #set inname = $jobtype.coll.name
+        #set infile = $jobtype.coll
       #end if
 
-      perl $__tool_directory__/sum_fastqc.pl $jobtype.single $infile $inname > sum_fastqc.tab
+      perl $__tool_directory__/sum_fastqc.pl $infile > sum_fastqc.tab
 
     ]]></command>
     <inputs>
@@ -21,10 +21,10 @@
           <option value="col">Collection of raw FASTQC Files</option>
         </param>
         <when value="single">
-          <param name="file" type="text" format="text" label="Raw FASTQC" />
+          <param name="file" type="data" format="txt" label="Raw FASTQC" />
         </when>
         <when value="col">
-          <param name="coll" label="Raw FASTQC Collection" type="data_collection" format="text" collection_type="list" />
+          <param name="coll" label="Raw FASTQC Collection" type="data_collection" format="txt" collection_type="list" />
         </when>
       </conditional>
     </inputs>
@@ -36,6 +36,5 @@
 
     ]]></help>
      <citations>
-       }</citation>
     </citations>
 </tool>