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comparison pyCRAC/pyExtractLinesFromGTF.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 ="pyExtractLinesFromGTF" name="pyExtractLinesFromGTF">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pyExtractLinesFromGTF.py --gtf $addGTF.gtf --genes_file $g --attribute $attribute $v -o $out
7 </command>
8 <version_command>/usr/local/bin/pyExtractLinesFromGTF.py --version</version_command>
9 <inputs>
10 <conditional name="addGTF">
11 <param name="gtfFile" type="select" label="Choose GTF File from">
12 <option value="default" selected="true">Defaults</option>
13 <option value="other">History</option>
14 </param>
15 <when value="default">
16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
17 <options from_data_table="pycrac_gtf"/>
18 </param>
19 </when>
20 <when value="other">
21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
22 </when>
23 </conditional>
24 <param format="txt" name="g" type="data" label="File containing gene list --genes_file" help="Tabular file with 1 column of gene or annotation names"/>
25 <param name="attribute" type="select" label="Select the attribute to extract names from --attribute">
26 <option value="gene_name" selected="true">gene_name</option>
27 <option value="gene_id">gene_id</option>
28 <option value="transcript_name">transcript_name</option>
29 <option value="transcript_id">transcript_id</option>
30 </param>
31 <param name="v" type="select" label="Extract lines from GTF that -v">
32 <option value="" selected="true">Match the gene file</option>
33 <option value="-v">Do not match in gene fil</option>
34 </param>
35 <param name="label" type="text" format="txt" size="30" value="pyExtractLinesFromGTF" label="Enter output file label -o" />
36 </inputs>
37
38 <outputs>
39 <data format="gtf" name="out" label="${label.value}.gtf"/>
40 </outputs>
41 <help>
42 .. class:: infomark
43
44 **pyExtractLinesFromGTF**
45
46 pyExtractLinesFromGTF is part of the pyCRAC_ package. Extracts lines from a GTF file that contain gene names of interest.
47
48
49 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
50
51 ------
52
53 **Parameter list**
54
55 Options::
56
57 --gtf=Yourfavoritegtf.gtf
58 type the path to the gtf file that you want to use. By
59 default it expects data from the standard input.
60 -g FILE, --genes_file=FILE
61 name of your gene list or annotations list file (1
62 column)
63 -o OUTFILE, --outfile=OUTFILE
64 type the name and path of the file you want to write
65 the output to. Default is standard output
66 -a ATTRIBUTE, --attribute=ATTRIBUTE
67 from which attribute do you want to extract names?
68 Choices: gene_name, gene_id, transcript_name,
69 transcript_id
70 -v
71 similar to grep -v option. Remove the genes from the
72 GTF that are in the gene list
73
74
75
76 </help>
77 </tool>