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comparison sum_fastqc-b769c810924e/sum_fastqc.xml @ 0:17652c6a7517 draft

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author estrain
date Wed, 17 Oct 2018 11:09:06 -0400
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1 <tool id="sum_fastqc" name="sum_fastqc" version="0.2">
2 <requirements>
3 </requirements>
4 <command detect_errors="exit_code"><![CDATA[
5
6 #if $jobtype.select == "single"
7 #set inname = $jobtype.file
8 #set infile = $jobtype.file
9 perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile > sum_fastqc.tab
10 #else if $jobtype.select == "col"
11 #set inname = $jobtype.coll.name
12 #set infile = $jobtype.coll.forward
13 #set infile2 = $jobtype.coll.reverse
14 perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile $infile2 > sum_fastqc.tab;
15 #end if
16
17 ]]></command>
18 <inputs>
19 <conditional name="jobtype">
20 <param name="select" type="select" label="Select Input">
21 <option value="single">Raw FASTQC output File</option>
22 <option value="col">Pair of raw FASTQC Files</option>
23 </param>
24 <when value="single">
25 <param name="file" type="data" format="txt" label="Raw FASTQC" />
26 </when>
27 <when value="col">
28 <param name="coll" label="Raw FASTQC pair" type="data_collection" format="txt" collection_type="paired" />
29 </when>
30 </conditional>
31 <conditional name="qset">
32 <param name="selectq" type="select" label="Single or multiple Q scores">
33 <option value="single">Single Q score</option>
34 <option value="mul">Multiple Q scores</option>
35 </param>
36 <when value="single">
37 <param name="qscore" type="integer" label="Q score threshold (i.e. reads >= Q score)" value="30">
38 <validator type="in_range" message="Must be integer(0,40)." min="0" max="40"/>
39 </param>
40 </when>
41 <when value="mul">
42 <param name="qscore" type="text" label="Comma delimited Q score list (e.g. 25,30,35)" value="30"/>
43 </when>
44 </conditional>
45 </inputs>
46 <outputs>
47 <data format="tabular" name="FASTQC Summary" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.tab"/>
48 </outputs>
49
50 <help><![CDATA[
51
52 ]]></help>
53 <citations>
54 </citations>
55 </tool>