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comparison tools/cgatools17/listvariants_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 64017ce705b6
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0:751b62d30ae1 1:3a2e0f376f26
1 <tool id="cg_listvariant" name="ListVariants" version="1.7.1">
2
3 <description>Lists all variants present in CG var or masterVar file</description>
4
5 <requirements>
6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements>
8
9 <command> <!--run executable-->
10 echo \$PATH;
11 cgatools | head -1;
12 cgatools listvariants
13 --beta
14 --reference ${crr.fields.crr_path}
15 --output $output
16 #if $include_list.listing == "yes" <!--only added when yes-->
17 --variant-listing $include_list.list
18 #end if
19 $longvar
20 --variants
21 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
22 ${v.input}
23 #end for
24
25
26 </command>
27
28 <inputs>
29 <!--form field to select crr file-->
30 <param name="crr" type="select" label="Reference genome (.crr file)">
31 <options from_data_table="cg_anno_files" />
32 </param>
33
34 <conditional name="file_types">
35 <param name="file_type" type="select" label="Select the input file type">
36 <option value="var" selected="true">var files</option>
37 <option value="mastervar">mastervar files</option>
38 </param>
39 <when value="var">
40 <repeat name="varfiles" title="Variant files" min="1">
41 <param name="input" type="data" format="cg_var" label="Dataset"/>
42 </repeat>
43 </when>
44 <when value="mastervar">
45 <repeat name="varfiles" title="Variant files" min="1">
46 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
47 </repeat>
48 </when>
49 </conditional>
50
51 <param name="longvar" type="select" label="List long variants?">
52 <option value="" selected="true">no</option>
53 <option value="--list-long-variants">yes</option>
54 </param>
55
56 <conditional name="include_list">
57 <param name="listing" type="select" label="Include variant listing?">
58 <option value="no" selected="true">no</option>
59 <option value="yes">yes</option>
60 </param>
61 <when value="yes">
62 <param name="list" type="data" format="tabular" label="Variant listing"/>
63 </when>
64 </conditional>
65 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
66 </inputs>
67
68 <outputs>
69 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
70 </outputs>
71
72 <help>
73 **What it does**
74
75 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
76
77 **cgatools 1.7.1 Documentation**
78
79 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
80
81 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
82
83 **Command line reference**::
84
85 COMMAND NAME
86 listvariants - Lists the variants present in a variant file.
87
88 DESCRIPTION
89 Lists all called variants present in the specified variant files, in a
90 format suitable for processing by the testvariants command. The output is a
91 tab-delimited file consisting of the following columns:
92
93 variantId Sequential id assigned to each variant.
94 chromosome The chromosome of the variant.
95 begin 0-based reference offset of the beginning of the variant.
96 end 0-based reference offset of the end of the variant.
97 varType The varType as extracted from the variant file.
98 reference The reference sequence.
99 alleleSeq The variant allele sequence as extracted from the variant
100 file.
101 xRef The xRef as extrated from the variant file.
102
103 OPTIONS
104 -h [ --help ]
105 Print this help message.
106
107 --beta
108 This is a beta command. To run this command, you must pass the --beta
109 flag.
110
111 --reference arg
112 The reference crr file.
113
114 --output arg (=STDOUT)
115 The output file (may be omitted for stdout).
116
117 --variants arg
118 The input variant files (may be positional args).
119
120 --variant-listing arg
121 The output of another listvariants run, to be merged in to produce the
122 output of this run.
123
124 --list-long-variants
125 In addition to listing short variants, list longer variants as well
126 (10's of bases) by concatenating nearby calls.
127
128 SUPPORTED FORMAT_VERSION
129 0.3 or later
130 </help>
131 </tool>