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date Thu, 27 Sep 2012 13:37:59 -0400
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1 <tool id="cg_snpdiff" name="snpdiff 1.6" version="1.0.1">
2 <!--
3 This tool creates a GUI for the snpdiff function of cgatools from Complete Genomics, Inc.
4 written 6-18-2012 by bcrain@completegenomics.com
5 updated 8-13-2012 by bcrain@completegenomics.com
6 -->
7
8 <description>compares snp calls to var or masterVar file.</description> <!--adds description in toolbar-->
9
10 <command> <!--run executable-->
11 <!-- print version of cgatools to STDOUT-->
12 cgatools | head -1;
13
14 <!-- print command lines to STDOUT-->
15 echo "cgatools snpdiff
16 --reference $crr.fields.path
17 --variants $data_sources.varfile
18 --genotypes $genotype
19 --output-prefix cg_
20 --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
21 ";
22
23 <!-- execute cgatools-->
24 cgatools snpdiff
25 --reference $crr.fields.path
26 --variants $data_sources.varfile
27 --genotypes $genotype
28 --output-prefix cg_
29 --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
30
31 </command>
32
33 <outputs>
34 <data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="${tool.name} Output">
35 <filter>(report1 == 'Output')</filter>
36 </data>
37 <data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="${tool.name} Verbose">
38 <filter>(report2 == 'Verbose')</filter>
39 </data>
40 <data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="${tool.name} Stats">
41 <filter>(report3 == 'Stats')</filter>
42 </data>
43 </outputs>
44
45 <inputs>
46 <!--form field to select crr file-->
47 <param name="crr" type="select" label="Reference genome (.crr file)">
48 <options from_data_table="cg_crr_files" />
49 </param>
50
51 <!--conditional to select data in/outside galaxy-->
52 <conditional name="data_sources">
53 <param name="data_source" type="select" label="Where is the input var or masterVar file?">
54 <option value="in" selected="true">imported into Galaxy</option>
55 <option value="out">located outside Galaxy (data on server or mounted drive)</option>
56 </param>
57
58 <!--form field to select input file-->
59 <when value="in">
60 <param name="varfile" type="data" format="cg_var,cg_mastervar" label="Var or masterVar file">
61 <validator type="dataset_ok_validator" />
62 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
63 metadata_name="dbkey" metadata_column="1"
64 message="cgatools is not currently available for this build."/>
65 </param>
66 </when>
67
68 <!--form field to enter input file-->
69 <when value="out">
70 <param name="varfile" type="text" label="Var or masterVar file (/path/file)" size="40" help="Var or masterVar file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2">
71 <validator type="empty_field" message="You must supply a var or masterVar file"/>
72 </param>
73 </when>
74 </conditional>
75
76 <!--param to select genotypes file input-->
77 <param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at least the following columns: Chromosome, Offset0Based, Genotypes (Optional)">
78 <validator type="dataset_ok_validator" />
79 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
80 metadata_name="dbkey" metadata_column="1"
81 message="cgatools is not currently available for this build."/>
82 <!--<validator type="expression" message="Dataset does not match selected build.">value.dbkey == $crr.fields.dbkey</validator>-->
83 </param>
84
85 <!--params to select reports-->
86 <param name="report1" type="select" label="Create report Output">
87 <option value="">no</option>
88 <option value="Output" selected="true">yes</option>
89 </param>
90 <param name="report2" type="select" label="Create report Verbose">
91 <option value="">no</option>
92 <option value="Verbose">yes</option>
93 </param>
94 <param name="report3" type="select" label="Create report Stats">
95 <option value="">no</option>
96 <option value="Stats">yes</option>
97 </param>
98 </inputs>
99
100 <help>
101
102 **What it does**
103
104 This tool ompares snp calls to a Complete Genomics variant file.
105
106 **cgatools 1.6.0 Documentation**
107
108 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
109
110 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
111
112 **Command line reference**::
113
114 COMMAND NAME
115 snpdiff - Compares snp calls to a Complete Genomics variant file.
116
117 DESCRIPTION
118 Compares the snp calls in the "genotypes" file to the calls in a Complete
119 Genomics variant file. The genotypes file is a tab-delimited file with at
120 least the following columns (additional columns may be given):
121
122 Chromosome (Required) The name of the chromosome.
123 Offset0Based (Required) The 0-based offset in the chromosome.
124 GenotypesStrand (Optional) The strand of the calls in the Genotypes
125 column (+ or -, defaults to +).
126 Genotypes (Optional) The calls, one per allele. The following
127 calls are recognized:
128 A,C,G,T A called base.
129 N A no-call.
130 - A deleted base.
131 . A non-snp variation.
132
133 The output is a tab-delimited file consisting of the columns of the
134 original genotypes file, plus the following additional columns:
135
136 Reference The reference base at the given position.
137 VariantFile The calls made by the variant file, one per allele.
138 The character codes are the same as is described for
139 the Genotypes column.
140 DiscordantAlleles (Only if Genotypes is present) The number of
141 Genotypes alleles that are discordant with calls in
142 the VariantFile. If the VariantFile is described as
143 haploid at the given position but the Genotypes is
144 diploid, then each genotype allele is compared
145 against the haploid call of the VariantFile.
146 NoCallAlleles (Only if Genotypes is present) The number of
147 Genotypes alleles that were no-called by the
148 VariantFile. If the VariantFile is described as
149 haploid at the given position but the Genotypes is
150 diploid, then a VariantFile no-call is counted twice.
151
152 The verbose output is a tab-delimited file consisting of the columns of the
153 original genotypes file, plus the following additional columns:
154
155 Reference The reference base at the given position.
156 VariantFile The call made by the variant file for one allele (there is
157 a line in this file for each allele). The character codes
158 are the same as is described for the Genotypes column.
159 [CALLS] The rest of the columns are pasted in from the VariantFile,
160 describing the variant file line used to make the call.
161
162 The stats output is a comma-separated file with several tables describing
163 the results of the snp comparison, for each diploid genotype. The tables
164 all describe the comparison result (column headers) versus the genotype
165 classification (row labels) in different ways. The "Locus classification"
166 tables have the most detailed match classifications, while the "Locus
167 concordance" tables roll these match classifications up into "discordance"
168 and "no-call". A locus is considered discordant if it is discordant for
169 either allele. A locus is considered no-call if it is concordant for both
170 alleles but has a no-call on either allele. The "Allele concordance"
171 describes the comparison result on a per-allele basis.
172
173 OPTIONS
174 -h [ --help ]
175 Print this help message.
176
177 --reference arg
178 The input crr file.
179
180 --variants arg
181 The input variant file.
182
183 --genotypes arg
184 The input genotypes file.
185
186 --output-prefix arg
187 The path prefix for all output reports.
188
189 --reports arg (=Output,Verbose,Stats)
190 Comma-separated list of reports to generate. A report is one of:
191 Output The output genotypes file.
192 Verbose The verbose output file.
193 Stats The stats output file.
194
195 SUPPORTED FORMAT_VERSION
196 0.3 or later
197 </help>
198 </tool>