Mercurial > repos > estrain > sum_fastqc

changeset 1:52c14941b49f draft

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Uploaded
author estrain
date Tue, 16 Oct 2018 17:16:03 -0400
parents cce90961c022
children 226ce8aaa97a
files sum_fastqc.xml
diffstat 1 files changed, 41 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sum_fastqc.xml	Tue Oct 16 17:16:03 2018 -0400
@@ -0,0 +1,41 @@
+<tool id="sum_fastqc" name="sum_fastqc" version="0.1">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+      #if $jobtype.select == "single"
+        #set inname = $jobtype.single.name
+        #set infile = $jobtype.single
+      #else if $jobtype.select == "col"
+        #set inname = $jobtype.col.name
+        #set infile = $jobtype.col.coll
+      #end if
+
+      perl $__tool_directory__/sum_fastqc.pl $jobtype.single $infile $inname > sum_fastqc.tab
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Select Input">
+          <option value="single">Raw FASTQC Output File</option>
+          <option value="col">Collection of raw FASTQC Files</option>
+        </param>
+        <when value="single">
+          <param name="file" type="text" format="text" label="Raw FASTQC" />
+        </when>
+        <when value="col">
+          <param name="coll" label="Raw FASTQC Collection" type="data_collection" format="text" collection_type="list" />
+        </when>
+      </conditional>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="FASTQC Summary" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.tab"/>
+    </outputs>
+
+    <help><![CDATA[
+
+    ]]></help>
+     <citations>
+       }</citation>
+    </citations>
+</tool>