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comparison tools/cgatools17/fasta2crr.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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children 91e163b708d3
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0:751b62d30ae1 1:3a2e0f376f26
1 <tool id="fasta2crr" name="fasta-2-crr" version="1.7.1">
2 <description> Convert fasta sequences into a single reference crr file </description>
3
4 <requirements>
5 <requirement type="package" version="1">cgatools17</requirement>
6 </requirements>
7
8 <command>
9 cgatools | head -1;
10 cgatools fasta2crr
11 #for $f in $fastafiles
12 --input ${f.file}
13 #end for
14 --output $output
15 #if $circ != "None"
16 --circular $circ
17 #end if
18 </command>
19
20 <inputs>
21 <repeat name="fastafiles" title="FASTA File" min="1">
22 <param name="file" type="data" format="tsv" label="select input fasta file" />
23 </repeat>
24 <param name="circ" type="data" format="tsv,bz2" optional="true" label="select file containing comma-separated list of circular chromosome names"/>
25 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
26 </inputs>
27
28 <outputs>
29 <data format="crr" name="output" label="$fname ${tool.name} on ${on_string}"/>
30 </outputs>
31
32 <help>
33
34 **What it does**
35
36 This tool converts input FASTA sequences into a single reference CRR file.
37
38 **cgatools 1.7.1 Documentation**
39
40 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
41
42 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
43
44 **Command line reference**::
45
46 COMMAND NAME
47 fasta2crr - Converts fasta reference files to the crr format.
48
49 OPTIONS
50 -h [ --help ]
51 Print this help message.
52
53 --input arg
54 The input fasta files (may be passed in as arguments at the end of the
55 command, or omitted for stdin). Take care to specify the fasta files in
56 chromosome order; ordering is important. To work with human Complete
57 Genomics data, the chromosome order should be chr1...chr22, chrX, chrY,
58 chrM.
59
60 --output arg
61 The output crr file.
62
63 --circular arg
64 A comma-separated list of circular chromosome names. If ommitted,
65 defaults to chrM.
66
67 </help>
68 </tool>
69
70