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comparison pyCRAC/pyCalculateChromosomeLengths.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="pyCalculateChromosomeLengths" name="pyCalculateChromosomeLengths">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pyCalculateChromosomeLengths.py
7 -f $ftype.input
8 --file_type $ftype.filetype
9 -o $output </command>
10 <version_command>/usr/local/bin/pyCalculateChromosomeLengths.py --version</version_command>
11 <inputs>
12 <conditional name="ftype">
13 <param name="filetype" type="select" label="File type">
14 <option value="fasta" selected="true">Fasta</option>
15 <option value="tab">Tab</option>
16 </param>
17 <when value="fasta">
18 <param name="input" type="data" format="fasta" label="Input file" help="Fasta or Tab file"/>
19 </when>
20 <when value="tab">
21 <param name="input" type="data" format="tabular" label="Input file" help="Fasta or Tab file"/>
22 </when>
23 </conditional>
24 </inputs>
25 <param name="label" type="text" format="txt" size="30" value="pyCalculateChromosomeLengths" label="Enter output file label -o" />
26 <outputs>
27 <data name="output" format="txt" label="${label.value}.len"/>
28 </outputs>
29 <help>
30
31 .. class:: infomark
32
33 **pyCalculateChromosomeLengths**
34
35 pyCalculateChromosomeLengths is part of the pyCRAC_ package. Takes a genome sequence in fasta or tab format and generates a tab-delimited file showing chromosome name and chromosome length.
36
37 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
38
39 -------
40
41 **Parameter list**
42
43 Options::
44
45 -f chromosomes.fasta, --input_file=chromosomes.fasta
46 provide the name and path of your fasta or tab genomic
47 sequence file. Default is standard input.
48 --file_type=fasta
49 provide the file type (fasta or tab). Default is fasta
50
51 </help>
52 </tool>
53