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comparison tools/cgatools17/crr2fasta.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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0:751b62d30ae1 1:3a2e0f376f26
1 <tool id="crr2fasta" name="crr-2-fasta" 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 crr2fasta
11 #if $refcrr.reference == "custom":
12 --input $refcrr.customcrr
13 #else:
14 --input ${refcrr.reffile.fields.crr_path}
15 #end if
16 --output $output
17 --line-width $linewidth
18 </command>
19
20 <inputs>
21 <conditional name="refcrr">
22 <param name="reference" type="select" label="Reference">
23 <option value="builtin" > Built-in Reference CRR </option>
24 <option value="custom"> Custom CRR file </option>
25 </param>
26 <when value="builtin">
27 <param name="reffile" type="select" label="Reference">
28 <options from_data_table="cg_anno_files" />
29 </param>
30 </when>
31 <when value="custom">
32 <param name="customcrr" type="data" format="crr" label="Select custom crr file" />
33 </when>
34 </conditional>
35
36 <param name="linewidth" type="text" label="linewidth" size="15" value="50" />
37 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
38 </inputs>
39
40 <outputs>
41 <data format="txt" name="output" label="$fname ${tool.name} on ${on_string}"/>
42 </outputs>
43
44 <help>
45
46 **What it does**
47
48 This tool converts reference CRR files into the FASTA file format.
49
50 **cgatools 1.7.1 Documentation**
51
52 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
53
54 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
55
56 **Command line reference**::
57
58 COMMAND NAME
59 crr2fasta - Converts a crr reference file to the fasta format.
60
61 OPTIONS
62 -h [ --help ]
63 Print this help message.
64
65 --input arg
66 The input crr file (may be passed in as argument at the end of the
67 command).
68
69 --output arg (=STDOUT)
70 The output fasta file (may be omitted for stdout).
71
72 --line-width arg (=50)
73 The maximum width of a line of sequence.
74
75
76 </help>
77 </tool>
78
79