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comparison tools/cgatools17/decodeCRR.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="cg_decodecrr" name="DecodeCRR" version="1.7.1">
2
3 <description>retreives the sequence for a given range of a chromosome.</description>
4
5 <requirements>
6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements>
8
9 <command>
10 cgatools | head -1;
11 cgatools decodecrr
12 #if $refcrr.reference == "custom":
13 --reference $refcrr.customcrr
14 #else:
15 --reference ${refcrr.reffile.fields.crr_path}
16 #end if
17 --output $output
18 --range $range
19 </command>
20
21 <inputs>
22 <conditional name="refcrr">
23 <param name="reference" type="select" label="Reference">
24 <option value="builtin" > Built-in Reference CRR </option>
25 <option value="custom"> Custom CRR file </option>
26 </param>
27 <when value="builtin">
28 <param name="reffile" type="select" label="Reference">
29 <options from_data_table="cg_anno_files" />
30 </param>
31 </when>
32 <when value="custom">
33 <param name="customcrr" type="data" format="crr" label="Select custom crr file" />
34 </when>
35 </conditional>
36
37 <param name="range" type="text" label="Select range" size="15" help="chr:begin-end e.g. chr4:30722030-30726957" />
38 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
39 </inputs>
40
41 <outputs>
42 <data format="txt" name="output" label="$fname ${tool.name} on ${on_string}"/>
43 </outputs>
44
45 <help>
46
47 **What it does**
48
49 Retrieves the sequence for a given range of a chromosome.
50
51 **cgatools 1.7.1 Documentation**
52
53 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
54
55 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
56
57 **Command line reference**::
58
59 COMMAND NAME
60 decodecrr - Prints the reference sequence for a given reference range.
61
62 OPTIONS
63 -h [ --help ]
64 Print this help message.
65
66 --reference arg
67 The reference crr file (may be passed in as argument at the end of the
68 command).
69
70 --output arg (=STDOUT)
71 The output file (may be omitted for stdout).
72
73 --range arg
74 The range of bases to print (chr,begin,end or chr:begin-end).
75
76 </help>
77 </tool>
78