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date Thu, 27 Sep 2012 13:37:59 -0400
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1 <tool id="cg_testvariants" name="testvariants(beta) 1.6" version="1.0.1">
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 updated 8-14-2012 by bcrain@completegenomics.com
6 -->
7
8 <description>test for the presence of variants</description>
9
10 <command>
11 <!-- print version of cgatools to STDOUT-->
12 cgatools | head -1;
13
14 <!-- print command lines to STDOUT-->
15 echo "cgatools testvariants --beta
16 --reference ${crr.fields.path}
17 --output $output
18 --input $listing
19 --variants
20 #if $data_sources.data_source == "in" <!--data in galaxy-->
21 #for $v in $data_sources.file_types.files <!--get each var/mastervar file-->
22 ${v.input}
23 #end for
24 #else <!--data outside galaxy-->
25 `cat $data_sources.list`
26 #end if
27 ";
28
29 <!-- execute cgatools-->
30 cgatools testvariants
31 --beta
32 --reference ${crr.fields.path}
33 --output $output
34 --input $listing
35 --variants
36 #if $data_sources.data_source == "in" <!--data in galaxy-->
37 #for $v in $data_sources.file_types.files <!--get each var/mastervar file-->
38 ${v.input}
39 #end for
40 #else <!--data outside galaxy-->
41 `cat $data_sources.list`
42 #end if
43 </command>
44
45 <outputs>
46 <data format="tabular" name="output" label="${tool.name} output"/>
47 </outputs>
48
49 <inputs>
50 <!--form field to select crr file-->
51 <param name="crr" type="select" label="Reference genome (.crr file)">
52 <options from_data_table="cg_crr_files" />
53 </param>
54
55 <!--form fields to select variant list-->
56 <param name="listing" type="data" format="tabular" label="Select variant list (output of listvariants)">
57 <validator type="dataset_ok_validator" />
58 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
59 metadata_name="dbkey" metadata_column="1"
60 message="cgatools is not currently available for this build."/>
61 </param>
62
63 <!--conditional to select data in/outside galaxy-->
64 <conditional name="data_sources">
65 <param name="data_source" type="select" label="Where are the input files?">
66 <option value="in" selected="true">imported into Galaxy</option>
67 <option value="out">located outside Galaxy (data on server or mounted drive)</option>
68 </param>
69
70 <when value="in">
71 <!--conditional to select input file type-->
72 <conditional name="file_types">
73 <param name="file_type" type="select" label="Select the input file type">
74 <option value="var" selected="true">var files</option>
75 <option value="mastervar">masterVar files</option>
76 </param>
77
78 <!--form field to select variant files-->
79 <when value="var">
80 <repeat name="files" title="Var file" min="1">
81 <param name="input" type="data" format="cg_var" label="Dataset">
82 <validator type="dataset_ok_validator" />
83 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
84 metadata_name="dbkey" metadata_column="1"
85 message="cgatools is not currently available for this build."/>
86 </param>
87 </repeat>
88 </when>
89
90 <!--form field to select masterVar files-->
91 <when value="mastervar">
92 <repeat name="files" title="MasterVar file" min="1">
93 <param name="input" type="data" format="cg_mastervar" label="Dataset">
94 <validator type="dataset_ok_validator" />
95 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
96 metadata_name="dbkey" metadata_column="1"
97 message="cgatools is not currently available for this build."/>
98 </param>
99 </repeat>
100 </when>
101 </conditional>
102 </when>
103
104 <!--form field to enter list file-->
105 <when value="out">
106 <param name="list" type="text" label="Enter file containing list of var or masterVar files (/path/file)" size="200" help="This file should contain a list of var or masterVar 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), the var or masterVar files can be compressed (gz, bz2).">
107 <validator type="empty_field" message="You must supply a file containing a list of var or masterVar files"/>
108 </param>
109 </when>
110 </conditional>
111 </inputs>
112
113 <help>
114
115 **What it does**
116
117 This tool uses the cgatools testvariants to test var or masterVar files for the presence of variants.
118
119 **cgatools 1.6.0 Documentation**
120
121 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
122
123 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
124
125 **Command line reference**::
126
127 COMMAND NAME
128 testvariants - Tests variant files for presence of variants.
129
130 DESCRIPTION
131 Tests variant files for presence of variants. The output is a tab-delimited
132 file consisting of the columns of the input variants file, plus a column
133 for each assembly results file that contains a character code for each
134 allele. The character codes have meaning as follows:
135
136 0 This allele of this genome is consistent with the reference at this
137 locus but inconsistent with the variant.
138 1 This allele of this genome has the input variant at this locus.
139 N This allele of this genome has no-calls but is consistent with the
140 input variant.
141
142 OPTIONS
143 -h [ --help ]
144 Print this help message.
145
146 --beta
147 This is a beta command. To run this command, you must pass the --beta
148 flag.
149
150 --reference arg
151 The reference crr file.
152
153 --input arg (=STDIN)
154 The input variants to test for.
155
156 --output arg (=STDOUT)
157 The output file (may be omitted for stdout).
158
159 --variants arg
160 The input variant files (may be passed in as arguments at the end of
161 the command).
162
163 SUPPORTED FORMAT_VERSION
164 0.3 or later
165 </help>
166 </tool>