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comparison pyCRAC/pyCheckGTFfile.xml @ 0:19b20927172d draft

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author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
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1 <tool id ="pyCheckGTFfile" name="pyCheckGTFfile">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pyCheckGTFfile.py --gtf $addGTF.gtf -o $out
7 </command>
8 <version_command>/usr/local/bin/pyCheckGTFfile.py --version</version_command>
9 <inputs>
10 <conditional name="addGTF">
11 <param name="gtfFile" type="select" label="Choose GTF File from">
12 <option value="default" selected="true">Defaults</option>
13 <option value="other">History</option>
14 </param>
15 <when value="default">
16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
17 <options from_data_table="pycrac_gtf"/>
18 </param>
19 </when>
20 <when value="other">
21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
22 </when>
23 </conditional>
24 <param name="label" type="text" format="txt" size="30" value="pyCheckGTFfile" label="Enter output file label -o" />
25 </inputs>
26
27 <outputs>
28 <data format="gtf" name="out" label="${label.value}.gtf"/>
29 </outputs>
30 <help>
31 .. class:: infomark
32
33 **pyCheckGTFfile**
34
35 pyCheckGTFfile is part of the pyCRAC_ package. Renames duplicated gene names in your GTF annotation file.
36
37 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
38
39 ------
40
41 **Parameter list**
42
43 Options::
44
45 --gtf=gtf input file
46 type the path to the gtf file that you want to use.
47 -o FILE, --output=FILE
48 Optional. Specify the name of the output file. Default
49 is standard output. Make sure it has the .gtf
50 extension!
51
52 </help>
53 </tool>