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comparison pyCRAC/pyFasta2tab.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="pyFasta2Tab" name="pyFasta2Tab">
2 <description>converter</description>
3 <requirements>
4 <requirement type="package">pyCRAC</requirement>
5 </requirements>
6 <command interpreter="python">/usr/local/bin/pyFasta2tab.py -f $input -o $output
7 </command>
8 <version_command>/usr/local/bin/pyFasta2tab.py --version</version_command>
9 <inputs>
10 <param name="input" type="data" format="fasta" label="Fasta file -f"/>
11 </inputs>
12 <param name="label" type="text" format="txt" size="30" value="pyFasta2Tab" label="Enter output file label -o" />
13 <outputs>
14 <data name="output" format="tabular" label="${label.value}.tab"/>
15 </outputs>
16 <help>
17
18 .. class:: infomark
19
20 **pyFasta2Tab**
21
22 pyFasta2Tab is part of the pyCRAC_ package. Converts fasta to tabular format. Is used to convert your reference sequences in fasta format to the tabular format that pyCRAC uses for almost all tools.
23
24 Example::
25
26 >sequence1
27 ATAGGATACATAACCATATTATGAGACC
28
29 Is converted into::
30
31 sequence1 ATAGGATACATAACCATATTATGAGACC
32
33 The pyCRAC package lo
34
35 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
36
37 -------
38
39 **Parameter list**
40
41 Options::
42
43 -f fasta_file, --input_file=fasta_file
44 provide the name and path of your fasta input file.
45 Default is standard input.
46
47
48
49 </help>
50 </tool>
51