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comparison pyCRAC/pyGetGTFSources.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 ="pyGetGTFSources" name="pyGetGTFSources">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pyGetGTFSources.py --gtf $addGTF.gtf --count -o $out
7 </command>
8 <version_command>/usr/local/bin/pyGetGTFSources.py --version</version_command>
9 <inputs>
10 <conditional name="addGTF">
11 <param name="gtfFile" type="select" label="Choose GTF File from">
12 <option value="default" selected="true">Defaults</option>
13 <option value="other">History</option>
14 </param>
15 <when value="default">
16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
17 <options from_data_table="pycrac_gtf"/>
18 </param>
19 </when>
20 <when value="other">
21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
22 </when>
23 </conditional>
24 <param name="count" type="select" label="Count occurences of each annotation --count">
25 <option value="" selected="true">No</option>
26 <option value="--count">Yes</option>
27 </param>
28 <param name="label" type="text" format="txt" size="30" value="GTF sources list" label="Enter output file label -o" />
29 </inputs>
30
31 <outputs>
32 <data format="tabular" name="out" label="${label.value}.txt"/>
33 </outputs>
34 <help>
35 .. class:: infomark
36
37 **pyGetGTFSources**
38
39 pyGetGTFSources is part of the pyCRAC_ package. Extracts source names from the second column in a GTF file.
40
41
42 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
43
44 ------
45
46 **Parameter list**
47
48 Options::
49
50 --gtf=Yourfavoritegtf.gtf
51 type the path to the gtf file that you want to use. By
52 default it expects data from the standard input
53 -o OUTFILE, --outfile=OUTFILE
54 type the name and path of the file you want to write
55 the output to. Default is standard output
56 --count with this flag you the program will count the
57 occurence for each source/annotation in the gtf file
58
59
60
61
62 </help>
63 </tool>