diff sum_fastqc.xml @ 6:9a9fdfef8b90 draft

Added option for multiple Q scores

--- a/sum_fastqc.xml	Tue Oct 16 21:59:38 2018 -0400
+++ b/sum_fastqc.xml	Wed Oct 17 07:11:24 2018 -0400
@@ -6,31 +6,42 @@
       #if $jobtype.select == "single"
         #set inname = $jobtype.file
         #set infile = $jobtype.file
-        perl $__tool_directory__/sum_fastqc.pl "$inname" $qscore $infile > sum_fastqc.tab
+        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" $qscore $infile $infile2 > sum_fastqc.tab;
+        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="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" />
+          <param name="coll" label="Raw FASTQC pair" type="data_collection" format="txt" collection_type="paired" />
         </when>
       </conditional>
-      <param name="qscore" type="integer" label="Q-Score Threshold" value="30">
-        <validator type="in_range" message="Must be integer(0,40)." min="0" max="40"/>
-      </param>
+      <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"/>