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comparison pyCRAC/pyGetGeneNamesFromGTF.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 ="pyGetGeneNamesFromGTF" name="pyGetGeneNamesFromGTF">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pyGetGeneNamesFromGTF.py --gtf $addGTF.gtf --attribute $attribute $count -o $out
7 </command>
8 <version_command>/usr/local/bin/pyGetGeneNamesFromGTF.py --version</version_command>
9 <inputs>
10 <conditional name="addGTF">
11 <param name="gtfFile" type="select" label="Choose GTF File from">
12 <option value="default" selected="true">Defaults</option>
13 <option value="other">History</option>
14 </param>
15 <when value="default">
16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
17 <options from_data_table="pycrac_gtf"/>
18 </param>
19 </when>
20 <when value="other">
21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
22 </when>
23 </conditional>
24 <param name="attribute" type="select" label="Select the attribute to extract names from --attribute">
25 <option value="gene_name" selected="true">gene_name</option>
26 <option value="gene_id">gene_id</option>
27 <option value="transcript_name">transcript_name</option>
28 <option value="transcript_id">transcript_id</option>
29 </param>
30 <param name="count" type="select" label="Count occurences of each annotation --count">
31 <option value="" selected="true">No</option>
32 <option value="--count">Yes</option>
33 </param>
34 <param name="label" type="text" format="txt" size="30" value="GTF gene list" label="Enter output file label -o" />
35 </inputs>
36
37 <outputs>
38 <data format="tabular" name="out" label="${label.value}.txt"/>
39 </outputs>
40 <help>
41 .. class:: infomark
42
43 **pyGetGeneNamesFromGTF**
44
45 pyGetGeneNamesFromGTF is part of the pyCRAC_ package. Extracts and counts all gene names from a GTF file.
46
47 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
48
49 ------
50
51 **Parameter list**
52
53 Options::
54
55 --gtf=Yourfavoritegtf.gtf
56 type the path to the gtf file that you want to use. By
57 default it expects data from the standard input.
58 -o OUTFILE, --outfile=OUTFILE
59 type the name and path of the file you want to write
60 the output to. Default is standard output
61 -a ATTRIBUTE, --attribute=ATTRIBUTE
62 from which attribute do you want to extract names?
63 Choices: gene_name, gene_id, transcript_name,
64 transcript_id
65 --count
66 with this flag you the program will count the
67 occurence for each source/annotation in the gtf file
68
69
70 </help>
71 </tool>