# HG changeset patch
# User estrain
# Date 1539788991 14400
# Node ID bc939b04bb12d3028d4687aa4fbf0e452ed7bf0f
# Parent  7d62c324d642402b9fbae4adb46ca3aba57ed289
Uploaded

diff -r 7d62c324d642 -r bc939b04bb12 sum_fastqc.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sum_fastqc.xml	Wed Oct 17 11:09:51 2018 -0400
@@ -0,0 +1,55 @@
+<tool id="sum_fastqc" name="sum_fastqc" version="0.2">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+      #if $jobtype.select == "single"
+        #set inname = $jobtype.file
+        #set infile = $jobtype.file
+        perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile > sum_fastqc.tab
+      #else if $jobtype.select == "col"
+        #set inname = $jobtype.coll.name
+        #set infile = $jobtype.coll.forward
+        #set infile2 = $jobtype.coll.reverse
+        perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile $infile2 > sum_fastqc.tab;
+      #end if
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Select Input">
+          <option value="single">Raw FASTQC output File</option>
+          <option value="col">Pair of raw FASTQC Files</option>
+        </param>
+        <when value="single">
+          <param name="file" type="data" format="txt" label="Raw FASTQC" />
+        </when>
+        <when value="col">
+          <param name="coll" label="Raw FASTQC pair" type="data_collection" format="txt" collection_type="paired" />
+        </when>
+      </conditional>
+      <conditional name="qset">
+        <param name="selectq" type="select" label="Single or multiple Q scores">
+          <option value="single">Single Q score</option>
+          <option value="mul">Multiple Q scores</option>
+        </param>
+        <when value="single">
+          <param name="qscore" type="integer" label="Q score threshold (i.e. reads >= Q score)" value="30">
+            <validator type="in_range" message="Must be integer(0,40)." min="0" max="40"/>
+          </param>
+        </when>
+        <when value="mul">
+          <param name="qscore" type="text" label="Comma delimited Q score list (e.g. 25,30,35)" value="30"/>
+        </when>
+      </conditional>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="FASTQC Summary" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.tab"/>
+    </outputs>
+
+    <help><![CDATA[
+
+    ]]></help>
+     <citations>
+    </citations>
+</tool>