Mercurial > repos > morinlab > calc_cnsegments
comparison calc_cnsegements_titan.xml @ 0:c6e48c6ac606 draft default tip
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/calc_cnsegments commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author | morinlab |
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date | Tue, 11 Oct 2016 14:16:32 -0400 |
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-1:000000000000 | 0:c6e48c6ac606 |
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1 <tool id="calc_cnsegments" name="calc_cnsegements" version="0.0.1"> | |
2 <description> | |
3 Calculate Copy Number Segments from TITAN output | |
4 </description> | |
5 <command> | |
6 <![CDATA[ | |
7 perl $__tool_directory__/calc_cnsegements_titan.pl | |
8 | |
9 #if $sampleid_source.sampleid_selector == "bamfile": | |
10 -id \$(basename $sampleid_source.sample_id | sed 's/.bam$//g' ) | |
11 #else: | |
12 -id $sampleid_source.sample_id | |
13 #end if | |
14 | |
15 -o $outfile | |
16 -s $symmetric | |
17 -igv $outIGV | |
18 -i $infile | |
19 | |
20 ]]> | |
21 </command> | |
22 <inputs> | |
23 <conditional name="sampleid_source"> | |
24 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select"> | |
25 <option value="bamfile">Bam File Name</option> | |
26 <option value="manual">Manual</option> | |
27 </param> | |
28 <when value="bamfile"> | |
29 <param type="data" format="bam" name="sample_id" label="Sequence Alignment File"/> | |
30 </when> | |
31 <when value="manual"> | |
32 <param name="sample_id" type="text" label="Sample ID (Name)"/> | |
33 </when> | |
34 </conditional> | |
35 <param type="data" format="txt" name="infile" label="SNP Summary Information (TITAN Output)"/> | |
36 <param type="boolean" name="symmetric" label="Symmetric" checked="yes" truevalue="1" falsevalue="0"/> | |
37 </inputs> | |
38 <outputs> | |
39 <data format="txt" name="outfile"/> | |
40 <data format="seg" name="outIGV"/> | |
41 </outputs> | |
42 </tool> |