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comparison cgatools/tools/cgatools_1.5/testvariants.xml @ 0:8ff0e55a0fc9 draft default tip

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author completegenomics
date Fri, 22 Jun 2012 15:53:08 -0400
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1 <tool id="cg_testvariants" name="testvariants(beta) 1.5" version="1.0.0">
2 <!--
3 This tool creates a GUI for the testvariants function of cgatools from Complete Genomics, Inc.
4 written 6-18-2012 by bcrain@completegenomics.com
5 -->
6
7 <description>test for the presence of variants</description> <!--adds description in toolbar-->
8
9 <requirements>
10 <requirement type="binary">cgatools</requirement>
11 </requirements>
12
13 <command> <!--run executable-->
14 cgatools | head -1;
15 cgatools testvariants
16 --beta
17 --reference ${crr.fields.path}
18 --output $output
19 --input $listing
20 --variants
21 #if $file_types.data_sources.data_source == "in"
22 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
23 ${v.input}
24 #end for
25 #else
26 `cat $file_types.data_sources.varlist`
27 #end if
28 </command>
29
30 <outputs>
31 <data format="tabular" name="output" />
32 </outputs>
33
34 <inputs>
35 <!--form field to select crr file-->
36 <param name="crr" type="select" label="Reference genome (.crr file)">
37 <options from_data_table="cg_crr_files" />
38 </param>
39
40 <!--form fields to select variant list-->
41 <param name="listing" type="data" format="tabular" label="Select variant list">
42 <validator type="unspecified_build" />
43 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
44 metadata_name="dbkey" metadata_column="1"
45 message="cgatools is not currently available for this build."/>
46 </param>
47
48 <!--conditional to select input file type-->
49 <conditional name="file_types">
50 <param name="file_type" type="select" label="Select the input file type">
51 <option value="var" selected="true">var files</option>
52 <option value="mastervar">mastervar files</option>
53 </param>
54
55 <when value="var">
56 <!--conditional to select variant file input-->
57 <conditional name="data_sources">
58 <param name="data_source" type="select" label="Where are the input var files?">
59 <option value="in" selected="true">imported into Galaxy</option>
60 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
61 </param>
62 <when value="in">
63 <!--form field to select variant files-->
64 <repeat name="varfiles" title="Variant files">
65 <param name="input" type="data" format="cg_var" label="Dataset">
66 <validator type="unspecified_build" />
67 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
68 metadata_name="dbkey" metadata_column="1"
69 message="cgatools is not currently available for this build."/>
70 </param>
71 </repeat>
72 </when>
73 <when value="out">
74 <!--form field to select crr file-->
75 <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="This file should contain a list of var files, one per line in the format /path/varfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2), var files can be compressed (gz, bz2)."/>
76 </when>
77 </conditional>
78 </when>
79
80 <when value="mastervar">
81 <!--conditional to select variant file input-->
82 <conditional name="data_sources">
83 <param name="data_source" type="select" label="Where are the input mastervar files?">
84 <option value="in" selected="true">imported into Galaxy</option>
85 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
86 </param>
87 <when value="in">
88 <!--form field to select variant files-->
89 <repeat name="varfiles" title="Variant files">
90 <param name="input" type="data" format="cg_mastervar" label="Dataset">
91 <validator type="unspecified_build" />
92 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
93 metadata_name="dbkey" metadata_column="1"
94 message="cgatools is not currently available for this build."/>
95 </param>
96 </repeat>
97 </when>
98 <when value="out">
99 <!--form field to select crr file-->
100 <param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="This file should contain a list of mastervar files, one per line in the format /path/varfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2), mastervar files can be compressed (gz, bz2)."/>
101 </when>
102 </conditional>
103 </when>
104 </conditional>
105 </inputs>
106
107 <help>
108
109 **What it does**
110
111 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
112
113 **cgatools 1.5.0 Documentation**
114
115 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
116
117 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
118
119 **Command line reference**::
120
121 COMMAND NAME
122 testvariants - Tests variant files for presence of variants.
123
124 DESCRIPTION
125 Tests variant files for presence of variants. The output is a tab-delimited
126 file consisting of the columns of the input variants file, plus a column
127 for each assembly results file that contains a character code for each
128 allele. The character codes have meaning as follows:
129
130 0 This allele of this genome is consistent with the reference at this
131 locus but inconsistent with the variant.
132 1 This allele of this genome has the input variant at this locus.
133 N This allele of this genome has no-calls but is consistent with the
134 input variant.
135
136 OPTIONS
137 -h [ --help ]
138 Print this help message.
139
140 --beta
141 This is a beta command. To run this command, you must pass the --beta
142 flag.
143
144 --reference arg
145 The reference crr file.
146
147 --input arg (=STDIN)
148 The input variants to test for.
149
150 --output arg (=STDOUT)
151 The output file (may be omitted for stdout).
152
153 --variants arg
154 The input variant files (may be passed in as arguments at the end of
155 the command).
156
157 SUPPORTED FORMAT_VERSION
158 0.3 or later
159 </help>
160 </tool>