annotate pyCRAC/pyGetGeneNamesFromGTF.xml @ 0:19b20927172d draft

Uploaded
author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
19b20927172d Uploaded
swebb
parents:
diff changeset
1 <tool id ="pyGetGeneNamesFromGTF" name="pyGetGeneNamesFromGTF">
19b20927172d Uploaded
swebb
parents:
diff changeset
2 <requirements>
19b20927172d Uploaded
swebb
parents:
diff changeset
3 <requirement type="package">pyCRAC</requirement>
19b20927172d Uploaded
swebb
parents:
diff changeset
4 </requirements>
19b20927172d Uploaded
swebb
parents:
diff changeset
5 <command interpreter="python">
19b20927172d Uploaded
swebb
parents:
diff changeset
6 /usr/local/bin/pyGetGeneNamesFromGTF.py --gtf $addGTF.gtf --attribute $attribute $count -o $out
19b20927172d Uploaded
swebb
parents:
diff changeset
7 </command>
19b20927172d Uploaded
swebb
parents:
diff changeset
8 <version_command>/usr/local/bin/pyGetGeneNamesFromGTF.py --version</version_command>
19b20927172d Uploaded
swebb
parents:
diff changeset
9 <inputs>
19b20927172d Uploaded
swebb
parents:
diff changeset
10 <conditional name="addGTF">
19b20927172d Uploaded
swebb
parents:
diff changeset
11 <param name="gtfFile" type="select" label="Choose GTF File from">
19b20927172d Uploaded
swebb
parents:
diff changeset
12 <option value="default" selected="true">Defaults</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
13 <option value="other">History</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
14 </param>
19b20927172d Uploaded
swebb
parents:
diff changeset
15 <when value="default">
19b20927172d Uploaded
swebb
parents:
diff changeset
16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
19b20927172d Uploaded
swebb
parents:
diff changeset
17 <options from_data_table="pycrac_gtf"/>
19b20927172d Uploaded
swebb
parents:
diff changeset
18 </param>
19b20927172d Uploaded
swebb
parents:
diff changeset
19 </when>
19b20927172d Uploaded
swebb
parents:
diff changeset
20 <when value="other">
19b20927172d Uploaded
swebb
parents:
diff changeset
21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
19b20927172d Uploaded
swebb
parents:
diff changeset
22 </when>
19b20927172d Uploaded
swebb
parents:
diff changeset
23 </conditional>
19b20927172d Uploaded
swebb
parents:
diff changeset
24 <param name="attribute" type="select" label="Select the attribute to extract names from --attribute">
19b20927172d Uploaded
swebb
parents:
diff changeset
25 <option value="gene_name" selected="true">gene_name</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
26 <option value="gene_id">gene_id</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
27 <option value="transcript_name">transcript_name</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
28 <option value="transcript_id">transcript_id</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
29 </param>
19b20927172d Uploaded
swebb
parents:
diff changeset
30 <param name="count" type="select" label="Count occurences of each annotation --count">
19b20927172d Uploaded
swebb
parents:
diff changeset
31 <option value="" selected="true">No</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
32 <option value="--count">Yes</option>
19b20927172d Uploaded
swebb
parents:
diff changeset
33 </param>
19b20927172d Uploaded
swebb
parents:
diff changeset
34 <param name="label" type="text" format="txt" size="30" value="GTF gene list" label="Enter output file label -o" />
19b20927172d Uploaded
swebb
parents:
diff changeset
35 </inputs>
19b20927172d Uploaded
swebb
parents:
diff changeset
36
19b20927172d Uploaded
swebb
parents:
diff changeset
37 <outputs>
19b20927172d Uploaded
swebb
parents:
diff changeset
38 <data format="tabular" name="out" label="${label.value}.txt"/>
19b20927172d Uploaded
swebb
parents:
diff changeset
39 </outputs>
19b20927172d Uploaded
swebb
parents:
diff changeset
40 <help>
19b20927172d Uploaded
swebb
parents:
diff changeset
41 .. class:: infomark
19b20927172d Uploaded
swebb
parents:
diff changeset
42
19b20927172d Uploaded
swebb
parents:
diff changeset
43 **pyGetGeneNamesFromGTF**
19b20927172d Uploaded
swebb
parents:
diff changeset
44
19b20927172d Uploaded
swebb
parents:
diff changeset
45 pyGetGeneNamesFromGTF is part of the pyCRAC_ package. Extracts and counts all gene names from a GTF file.
19b20927172d Uploaded
swebb
parents:
diff changeset
46
19b20927172d Uploaded
swebb
parents:
diff changeset
47 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
19b20927172d Uploaded
swebb
parents:
diff changeset
48
19b20927172d Uploaded
swebb
parents:
diff changeset
49 ------
19b20927172d Uploaded
swebb
parents:
diff changeset
50
19b20927172d Uploaded
swebb
parents:
diff changeset
51 **Parameter list**
19b20927172d Uploaded
swebb
parents:
diff changeset
52
19b20927172d Uploaded
swebb
parents:
diff changeset
53 Options::
19b20927172d Uploaded
swebb
parents:
diff changeset
54
19b20927172d Uploaded
swebb
parents:
diff changeset
55 --gtf=Yourfavoritegtf.gtf
19b20927172d Uploaded
swebb
parents:
diff changeset
56 type the path to the gtf file that you want to use. By
19b20927172d Uploaded
swebb
parents:
diff changeset
57 default it expects data from the standard input.
19b20927172d Uploaded
swebb
parents:
diff changeset
58 -o OUTFILE, --outfile=OUTFILE
19b20927172d Uploaded
swebb
parents:
diff changeset
59 type the name and path of the file you want to write
19b20927172d Uploaded
swebb
parents:
diff changeset
60 the output to. Default is standard output
19b20927172d Uploaded
swebb
parents:
diff changeset
61 -a ATTRIBUTE, --attribute=ATTRIBUTE
19b20927172d Uploaded
swebb
parents:
diff changeset
62 from which attribute do you want to extract names?
19b20927172d Uploaded
swebb
parents:
diff changeset
63 Choices: gene_name, gene_id, transcript_name,
19b20927172d Uploaded
swebb
parents:
diff changeset
64 transcript_id
19b20927172d Uploaded
swebb
parents:
diff changeset
65 --count
19b20927172d Uploaded
swebb
parents:
diff changeset
66 with this flag you the program will count the
19b20927172d Uploaded
swebb
parents:
diff changeset
67 occurence for each source/annotation in the gtf file
19b20927172d Uploaded
swebb
parents:
diff changeset
68
19b20927172d Uploaded
swebb
parents:
diff changeset
69
19b20927172d Uploaded
swebb
parents:
diff changeset
70 </help>
19b20927172d Uploaded
swebb
parents:
diff changeset
71 </tool>