Mercurial > repos > completegenomics > cg_cgatools_linux
comparison cgatools/tools/cgatools_1.5/varfilter.xml @ 0:182426b32995 draft default tip
Uploaded
author | completegenomics |
---|---|
date | Mon, 18 Jun 2012 20:15:00 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:182426b32995 |
---|---|
1 <tool id="cg_varfilter" name="varfilter(beta) 1.5" version="1.0.0"> | |
2 <!-- | |
3 This tool creates a GUI for the varfilter function of cgatools from Complete Genomics, Inc. | |
4 The function is called via a Perl script vartools_wrapper.pl, designed to generate the correctly formated filters to append the input file on the command line. | |
5 written 6-18-2012 by bcrain@completegenomics.com | |
6 --> | |
7 | |
8 <description>copies input file, applying filters.</description> <!--adds description in toolbar--> | |
9 | |
10 <requirements> | |
11 <requirement type="binary">cgatools</requirement> | |
12 </requirements> | |
13 | |
14 <command interpreter="perl"> | |
15 cgatools | head -1; | |
16 varfilter_wrapper.pl | |
17 --reference $crr.fields.path | |
18 --output $output | |
19 --input $file_types.data_sources.input | |
20 #for $f in $filters | |
21 --zygosity $f.zygosity | |
22 --vartype $f.vartype | |
23 --varscorevaf x$f.varscorevaf | |
24 --varscoreeaf x$f.varscoreeaf | |
25 --varquality $f.varquality | |
26 #end for | |
27 </command> | |
28 | |
29 <outputs> | |
30 <data format="cg_var" name="output" /> | |
31 </outputs> | |
32 | |
33 <inputs> | |
34 <!--form field to select crr file--> | |
35 <param name="crr" type="select" label="Reference genome (.crr file)"> | |
36 <options from_data_table="cg_crr_files" /> | |
37 </param> | |
38 | |
39 <!--conditional to select input file type--> | |
40 <conditional name="file_types"> | |
41 <param name="file_type" type="select" label="Select the input file type"> | |
42 <option value="var" selected="true">var files</option> | |
43 <option value="mastervar">mastervar files</option> | |
44 </param> | |
45 | |
46 <when value="var"> | |
47 <!--conditional to select variant file input--> | |
48 <conditional name="data_sources"> | |
49 <param name="data_source" type="select" label="Where is the input var file?"> | |
50 <option value="in" selected="true">imported into Galaxy</option> | |
51 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option> | |
52 </param> | |
53 <when value="in"> | |
54 <!--form field to select variant files--> | |
55 <param name="input" type="data" format="cg_var" label="Var file"> | |
56 <validator type="unspecified_build" /> | |
57 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" | |
58 metadata_name="dbkey" metadata_column="1" | |
59 message="cgatools is not currently available for this build."/> | |
60 </param> | |
61 </when> | |
62 <when value="out"> | |
63 <!--form field to select crr file--> | |
64 <param name="input" type="text" label="Var file (/path/file)" size="200" help="Variant file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2"/> | |
65 </when> | |
66 </conditional> | |
67 </when> | |
68 | |
69 <when value="mastervar"> | |
70 <!--conditional to select variant file input--> | |
71 <conditional name="data_sources"> | |
72 <param name="data_source" type="select" label="Where is the input mastervar file?"> | |
73 <option value="in" selected="true">imported into Galaxy</option> | |
74 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option> | |
75 </param> | |
76 <when value="in"> | |
77 <!--form field to select variant files--> | |
78 <param name="input" type="data" format="cg_mastervar" label="Mastervar file"> | |
79 <validator type="unspecified_build" /> | |
80 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" | |
81 metadata_name="dbkey" metadata_column="1" | |
82 message="cgatools is not currently available for this build."/> | |
83 </param> | |
84 </when> | |
85 <when value="out"> | |
86 <!--form field to select crr file--> | |
87 <param name="input" type="text" label="Mastervar file (/path/file)" size="200" help="Mastervar file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2"/> | |
88 </when> | |
89 </conditional> | |
90 </when> | |
91 </conditional> | |
92 | |
93 <!-- formfields to add filters --> | |
94 <repeat name="filters" title="Filter"> | |
95 <param name="zygosity" type="select" label="Filter out call (set to no-call) IF locus IS"> | |
96 <option value="NA">- all loci -</option> | |
97 <option value="hom">homozygous</option> | |
98 <option value="het">heterzygous</option> | |
99 </param> | |
100 | |
101 <param name="vartype" type="select" label="AND varType IS"> | |
102 <option value="NA">- any varType -</option> | |
103 <option value="snp">snp</option> | |
104 <option value="ins">ins</option> | |
105 <option value="del">del</option> | |
106 <option value="sub">sub</option> | |
107 <option value="ref">ref</option> | |
108 </param> | |
109 | |
110 <param name="varscorevaf" type="text" label="AND varScoreVAF IS LESS THAN"/> | |
111 <param name="varscoreeaf" type="text" label="AND varScoreEAF IS LESS THAN"/> | |
112 | |
113 <param name="varquality" type="select" label="AND varQuality IS NOT"> | |
114 <option value="NA"> </option> | |
115 <option value="VQHigh">VQHigh</option> | |
116 <option value="VQLOW">VQLOW</option> | |
117 </param> | |
118 </repeat> | |
119 </inputs> | |
120 | |
121 <help> | |
122 | |
123 **What it does** | |
124 | |
125 This tool copies input var file or masterVar file to output, applying specified filters. | |
126 | |
127 **cgatools 1.5.0 Documentation** | |
128 | |
129 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf | |
130 | |
131 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf | |
132 | |
133 **Command line reference**:: | |
134 | |
135 COMMAND NAME | |
136 varfilter - Copies input var file or masterVar file to output, applying | |
137 specified filters. | |
138 | |
139 DESCRIPTION | |
140 Copies input var file or masterVar file to output, applying specified | |
141 filters (which are available to all cgatools commands that read a var file | |
142 or masterVar file as input). Filters are specified by appending the filter | |
143 specification to the var file name on the command line. For example: | |
144 | |
145 /path/to/var.tsv.bz2#varQuality!=VQHIGH | |
146 | |
147 The preceding example filters out any calls marked as VQLOW. The filter | |
148 specification follows the "#" sign, and consists of a list of filters to | |
149 apply, separated by a comma. Each filter is a colon-separated list of call | |
150 selectors. Any scored call that passes all the colon-separated call | |
151 selectors for one or more of the comma-separated filters is turned into a | |
152 no-call. The following call selectors are available: | |
153 | |
154 hom Selects only calls in homozygous loci. | |
155 het Selects any scored call not selected by the hom selector. | |
156 varType=XX Selects calls whose varType is XX. | |
157 varScoreVAF<XX Selects calls whose varScoreVAF<XX. | |
158 varScoreEAF<XX Selects calls whose varScoreEAF<XX. | |
159 varQuality!=XX Selects calls whose varQuality is not XX. | |
160 | |
161 Here is an example that filters homozygous SNPs with varScoreVAF < 25 and | |
162 heterozygous insertions with varScoreEAF < 50: | |
163 | |
164 | |
165 '/path/to/var.tsv.bz2#hom:varType=snp:varScoreVAF<25,het:varType=ins:varScoreEAF<50' | |
166 | |
167 | |
168 OPTIONS | |
169 -h [ --help ] | |
170 Print this help message. | |
171 | |
172 --beta | |
173 This is a beta command. To run this command, you must pass the --beta flag. | |
174 | |
175 --reference arg | |
176 The reference crr file. | |
177 | |
178 --input arg | |
179 The input var file or masterVar file (typically with filters specified). | |
180 | |
181 --output arg (=STDOUT) | |
182 The output file (may be omitted for stdout). | |
183 | |
184 SUPPORTED FORMAT_VERSION | |
185 0.3 or later | |
186 </help> | |
187 </tool> |