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comparison tools/cgatools17/testvariants_v17.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="cg_testvariants" name="TestVariants" version="1.7.1">
2
3 <description>Test for the presence of variants</description>
4
5 <requirements>
6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements>
8
9 <command> <!--run executable-->
10 cgatools | head -1;
11 cgatools testvariants
12 --beta
13 --reference ${crr.fields.crr_path}
14 --output $output
15 --input $listing
16 --variants
17 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
18 ${v.input}
19 #end for
20 </command>
21
22 <inputs>
23 <!--form field to select crr file-->
24 <param name="crr" type="select" label="Reference Build">
25 <options from_data_table="cg_anno_files" />
26 </param>
27
28 <!--form fields to select variant list-->
29 <param name="listing" type="data" format="tabular" label="Select variant list"/>
30
31 <!--conditional to select input file type-->
32 <conditional name="file_types">
33 <param name="file_type" type="select" label="Select the input file type">
34 <option value="var" selected="true">var files</option>
35 <option value="mastervar">mastervar files</option>
36 </param>
37 <when value="var">
38 <repeat name="varfiles" title="Variant files">
39 <param name="input" type="data" format="cg_var" label="Dataset"/>
40 </repeat>
41 </when>
42 <when value="mastervar">
43 <repeat name="varfiles" title="Variant files">
44 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
45 </repeat>
46 </when>
47 </conditional>
48
49 <!-- prefix for output file so you dont have to manually rename history items -->
50 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
51 </inputs>
52
53
54 <outputs>
55 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
56 </outputs>
57
58 <help>
59 **What it does**
60
61 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
62
63 **cgatools 1.7.1 Documentation**
64
65 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
66
67 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
68
69 **Command line reference**::
70
71 COMMAND NAME
72 testvariants - Tests variant files for presence of variants.
73
74 DESCRIPTION
75 Tests variant files for presence of variants. The output is a tab-delimited
76 file consisting of the columns of the input variants file, plus a column
77 for each assembly results file that contains a character code for each
78 allele. The character codes have meaning as follows:
79
80 0 This allele of this genome is consistent with the reference at this
81 locus but inconsistent with the variant.
82 1 This allele of this genome has the input variant at this locus.
83 N This allele of this genome has no-calls but is consistent with the
84 input variant.
85
86 OPTIONS
87 -h [ --help ]
88 Print this help message.
89
90 --beta
91 This is a beta command. To run this command, you must pass the --beta
92 flag.
93
94 --reference arg
95 The reference crr file.
96
97 --input arg (=STDIN)
98 The input variants to test for.
99
100 --output arg (=STDOUT)
101 The output file (may be omitted for stdout).
102
103 --variants arg
104 The input variant files (may be passed in as arguments at the end of
105 the command).
106
107 SUPPORTED FORMAT_VERSION
108 0.3 or later
109 </help>
110 </tool>