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comparison tools/cgatools17/snpdiff_v17.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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0:751b62d30ae1 1:3a2e0f376f26
1 <tool id="cg_snpdiff" name="SNPDiff" version="1.7.1">
2
3 <description>compares snp calls to a Complete Genomics variant file.</description>
4
5 <requirements>
6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements>
8
9 <command>
10 cgatools | head -1;
11 cgatools snpdiff
12 --reference ${crr.fields.crr_path}
13 --variants $varfile
14 --genotypes $genotype
15 --output-prefix cg_
16 --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
17 </command>
18
19 <inputs>
20 <param name="crr" type="select" label="Reference build">
21 <options from_data_table="cg_anno_files" />
22 </param>
23 <param name="varfile" type="data" format="cg_var" label="Var file"/>
24
25 <param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at least the following columns (additional columns may be given): Chromosome (Required), Offset0Based (Required), GenotypesStrand (Optional), Genotypes (Optional)"/>
26
27 <param name="report1" type="select" label="Create report Output">
28 <option value="">no</option>
29 <option value="Output">yes</option>
30 </param>
31 <param name="report2" type="select" label="Create report Verbose">
32 <option value="">no</option>
33 <option value="Verbose">yes</option>
34 </param>
35 <param name="report3" type="select" label="Create report Stats">
36 <option value="">no</option>
37 <option value="Stats">yes</option>
38 </param>
39 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
40 </inputs>
41
42 <outputs>
43 <data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="$fname ${tool.name} on ${on_string}: Output">
44 <filter>(report1 == 'Output')</filter>
45 </data>
46 <data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="$fname ${tool.name} on ${on_string}: Verbose">
47 <filter>(report2 == 'Verbose')</filter>
48 </data>
49 <data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="$fname ${tool.name} on ${on_string}: Stats">
50 <filter>(report3 == 'Stats')</filter>
51 </data>
52 </outputs>
53 <help>
54 **What it does**
55
56 This tool ompares snp calls to a Complete Genomics variant file.
57
58 **cgatools 1.7.1 Documentation**
59
60 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
61
62 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
63
64 **Command line reference**::
65
66 COMMAND NAME
67 snpdiff - Compares snp calls to a Complete Genomics variant file.
68
69 DESCRIPTION
70 Compares the snp calls in the "genotypes" file to the calls in a Complete
71 Genomics variant file. The genotypes file is a tab-delimited file with at
72 least the following columns (additional columns may be given):
73
74 Chromosome (Required) The name of the chromosome.
75 Offset0Based (Required) The 0-based offset in the chromosome.
76 GenotypesStrand (Optional) The strand of the calls in the Genotypes
77 column (+ or -, defaults to +).
78 Genotypes (Optional) The calls, one per allele. The following
79 calls are recognized:
80 A,C,G,T A called base.
81 N A no-call.
82 - A deleted base.
83 . A non-snp variation.
84
85 The output is a tab-delimited file consisting of the columns of the
86 original genotypes file, plus the following additional columns:
87
88 Reference The reference base at the given position.
89 VariantFile The calls made by the variant file, one per allele.
90 The character codes are the same as is described for
91 the Genotypes column.
92 DiscordantAlleles (Only if Genotypes is present) The number of
93 Genotypes alleles that are discordant with calls in
94 the VariantFile. If the VariantFile is described as
95 haploid at the given position but the Genotypes is
96 diploid, then each genotype allele is compared
97 against the haploid call of the VariantFile.
98 NoCallAlleles (Only if Genotypes is present) The number of
99 Genotypes alleles that were no-called by the
100 VariantFile. If the VariantFile is described as
101 haploid at the given position but the Genotypes is
102 diploid, then a VariantFile no-call is counted twice.
103
104 The verbose output is a tab-delimited file consisting of the columns of the
105 original genotypes file, plus the following additional columns:
106
107 Reference The reference base at the given position.
108 VariantFile The call made by the variant file for one allele (there is
109 a line in this file for each allele). The character codes
110 are the same as is described for the Genotypes column.
111 [CALLS] The rest of the columns are pasted in from the VariantFile,
112 describing the variant file line used to make the call.
113
114 The stats output is a comma-separated file with several tables describing
115 the results of the snp comparison, for each diploid genotype. The tables
116 all describe the comparison result (column headers) versus the genotype
117 classification (row labels) in different ways. The "Locus classification"
118 tables have the most detailed match classifications, while the "Locus
119 concordance" tables roll these match classifications up into "discordance"
120 and "no-call". A locus is considered discordant if it is discordant for
121 either allele. A locus is considered no-call if it is concordant for both
122 alleles but has a no-call on either allele. The "Allele concordance"
123 describes the comparison result on a per-allele basis.
124
125 OPTIONS
126 -h [ --help ]
127 Print this help message.
128
129 --reference arg
130 The input crr file.
131
132 --variants arg
133 The input variant file.
134
135 --genotypes arg
136 The input genotypes file.
137
138 --output-prefix arg
139 The path prefix for all output reports.
140
141 --reports arg (=Output,Verbose,Stats)
142 Comma-separated list of reports to generate. A report is one of:
143 Output The output genotypes file.
144 Verbose The verbose output file.
145 Stats The stats output file.
146
147 SUPPORTED FORMAT_VERSION
148 0.3 or later
149 </help>
150 </tool>