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comparison cgatools/tools/cgatools_1.5/listtestvariants.xml @ 0:3b8b80827fbe draft default tip

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date Fri, 22 Jun 2012 14:25:22 -0400
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1 <tool id="cg_listtestvariants" name="listvariants(beta)-testvariants(beta) 1.5" version="1.0.0">
2 <!--
3 This tool creates a GUI for the listvariants and testvariants functions of cgatools from Complete Genomics, Inc.
4 to be run consecutively with the same input files.
5 written 6-18-2012 by bcrain@completegenomics.com
6 -->
7
8 <description>performs listsvariants and testvariants consecutively</description> <!--adds description in toolbar-->
9
10 <requirements>
11 <requirement type="binary">cgatools</requirement>
12 </requirements>
13
14 <command> <!--run executable-->
15 cgatools | head -1;
16 cgatools listvariants
17 --beta
18 --reference ${crr.fields.path}
19 --output $output1
20 #if $include_list.listing == "yes" <!--only added when yes-->
21 --variant-listing $include_list.list
22 #end if
23 $longvar
24 --variants
25 #if $file_types.data_sources.data_source == "in"
26 #for $v in $file_types.data_sources.varfiles <!--get each var file-->
27 ${v.input}
28 #end for
29 #else
30 `cat $file_types.data_sources.varlist`
31 #end if
32 ;
33
34 cgatools testvariants
35 --beta
36 --reference ${crr.fields.path}
37 --output $output2
38 --input $output1
39 --variants
40 #if $file_types.data_sources.data_source == "in"
41 #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file-->
42 ${v.input}
43 #end for
44 #else
45 `cat $file_types.data_sources.varlist`
46 #end if
47 </command>
48
49 <outputs>
50 <data format="tabular" name="output1" label="listvariants output"/>
51 <data format="tabular" name="output2" label="testvariants output"/>
52 </outputs>
53
54 <inputs>
55 <!--form field to select crr file-->
56 <param name="crr" type="select" label="Reference genome (.crr file)">
57 <options from_data_table="cg_crr_files" />
58 </param>
59
60 <!--form field to select long variants option-->
61 <param name="longvar" type="select" label="List long variants?">
62 <option value="" selected="true">no</option>
63 <option value="--list-long-variants">yes</option>
64 </param>
65
66 <!--form fields to include existing variant list-->
67 <conditional name="include_list">
68 <param name="listing" type="select" label="Include variant listing?">
69 <option value="no" selected="true">no</option>
70 <option value="yes">yes</option>
71 </param>
72 <when value="yes">
73 <param name="list" type="data" format="tabular" label="Variant listing">
74 <validator type="unspecified_build" />
75 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
76 metadata_name="dbkey" metadata_column="1"
77 message="cgatools is not currently available for this build."/>
78 </param>
79 </when>
80 </conditional>
81
82 <!--conditional to select input file type-->
83 <conditional name="file_types">
84 <param name="file_type" type="select" label="Select the input file type">
85 <option value="var" selected="true">var files</option>
86 <option value="mastervar">mastervar files</option>
87 </param>
88
89 <when value="var">
90 <!--conditional to select variant file input-->
91 <conditional name="data_sources">
92 <param name="data_source" type="select" label="Where are the input var files?">
93 <option value="in" selected="true">imported into Galaxy</option>
94 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
95 </param>
96 <when value="in">
97 <!--form field to select variant files-->
98 <repeat name="varfiles" title="Variant files">
99 <param name="input" type="data" format="cg_var" label="Dataset">
100 <validator type="unspecified_build" />
101 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
102 metadata_name="dbkey" metadata_column="1"
103 message="cgatools is not currently available for this build."/>
104 </param>
105 </repeat>
106 </when>
107 <when value="out">
108 <!--form field to select crr file-->
109 <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)."/>
110 </when>
111 </conditional>
112 </when>
113
114 <when value="mastervar">
115 <!--conditional to select variant file input-->
116 <conditional name="data_sources">
117 <param name="data_source" type="select" label="Where are the input mastervar files?">
118 <option value="in" selected="true">imported into Galaxy</option>
119 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
120 </param>
121 <when value="in">
122 <!--form field to select variant files-->
123 <repeat name="varfiles" title="Variant files">
124 <param name="input" type="data" format="cg_mastervar" label="Dataset">
125 <validator type="unspecified_build" />
126 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
127 metadata_name="dbkey" metadata_column="1"
128 message="cgatools is not currently available for this build."/>
129 </param>
130 </repeat>
131 </when>
132 <when value="out">
133 <!--form field to select crr file-->
134 <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)."/>
135 </when>
136 </conditional>
137 </when>
138 </conditional>
139 </inputs>
140
141 <help>
142
143 **What it does**
144
145 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
146
147 **cgatools 1.5.0 Documentation**
148
149 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
150
151 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
152
153 **Command line reference**::
154
155 COMMAND NAME
156 listvariants - Lists the variants present in a variant file.
157
158 DESCRIPTION
159 Lists all called variants present in the specified variant files, in a
160 format suitable for processing by the testvariants command. The output is a
161 tab-delimited file consisting of the following columns:
162
163 variantId Sequential id assigned to each variant.
164 chromosome The chromosome of the variant.
165 begin 0-based reference offset of the beginning of the variant.
166 end 0-based reference offset of the end of the variant.
167 varType The varType as extracted from the variant file.
168 reference The reference sequence.
169 alleleSeq The variant allele sequence as extracted from the variant
170 file.
171 xRef The xRef as extrated from the variant file.
172
173 OPTIONS
174 -h [ --help ]
175 Print this help message.
176
177 --beta
178 This is a beta command. To run this command, you must pass the --beta
179 flag.
180
181 --reference arg
182 The reference crr file.
183
184 --output arg (=STDOUT)
185 The output file (may be omitted for stdout).
186
187 --variants arg
188 The input variant files (may be positional args).
189
190 --variant-listing arg
191 The output of another listvariants run, to be merged in to produce the
192 output of this run.
193
194 --list-long-variants
195 In addition to listing short variants, list longer variants as well
196 (10's of bases) by concatenating nearby calls.
197
198 SUPPORTED FORMAT_VERSION
199 0.3 or later
200
201
202
203 COMMAND NAME
204 testvariants - Tests variant files for presence of variants.
205
206 DESCRIPTION
207 Tests variant files for presence of variants. The output is a tab-delimited
208 file consisting of the columns of the input variants file, plus a column
209 for each assembly results file that contains a character code for each
210 allele. The character codes have meaning as follows:
211
212 0 This allele of this genome is consistent with the reference at this
213 locus but inconsistent with the variant.
214 1 This allele of this genome has the input variant at this locus.
215 N This allele of this genome has no-calls but is consistent with the
216 input variant.
217
218 OPTIONS
219 -h [ --help ]
220 Print this help message.
221
222 --beta
223 This is a beta command. To run this command, you must pass the --beta
224 flag.
225
226 --reference arg
227 The reference crr file.
228
229 --input arg (=STDIN)
230 The input variants to test for.
231
232 --output arg (=STDOUT)
233 The output file (may be omitted for stdout).
234
235 --variants arg
236 The input variant files (may be passed in as arguments at the end of
237 the command).
238
239 SUPPORTED FORMAT_VERSION
240 0.3 or later
241 </help>
242 </tool>