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comparison snpEff.xml @ 0:c07c403fc470

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author jjohnson
date Thu, 17 Jan 2013 16:31:12 -0500
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1 <tool id="snpEff" name="SnpEff" version="3.1">
2 <description>Variant effect and annotation</description>
3 <!--
4 You will need to change the path to wherever your installation is.
5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
7 -->
8 <requirements>
9 <requirement type="package" version="3.1">snpEff</requirement>
10 </requirements>
11 <command>
12 export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
13 if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
14 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
15 fi;
16 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
17 <inputs>
18 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
19
20 <param name="inputFormat" type="select" label="Input format">
21 <option value="vcf">VCF</option>
22 <option value="txt">Tabular</option>
23 <option value="pileup">Pileup</option>
24 <option value="bed">BED</option>
25 </param>
26
27 <param name="outputFormat" type="select" label="Output format">
28 <option value="txt">Tabular</option>
29 <option value="vcf">VCF (only if input is VCF)</option>
30 <option value="bed">BED</option>
31 <option value="bedAnn">BED Annotations</option>
32 </param>
33
34 <param name="genomeVersion" type="select" label="Genome">
35 <options from_file="snpeffect_genomedb.loc">
36 <column name="name" index="1"/>
37 <column name="value" index="0"/>
38 </options>
39 </param>
40
41 <param name="udLength" type="select" label="Upstream / Downstream length">
42 <option value="0">No upstream / downstream intervals (0 bases)</option>
43 <option value="200">200 bases</option>
44 <option value="500">500 bases</option>
45 <option value="1000">1000 bases</option>
46 <option value="2000">2000 bases</option>
47 <option value="5000" selected="true">5000 bases</option>
48 <option value="10000">10000 bases</option>
49 <option value="20000">20000 bases</option>
50 </param>
51
52 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
53 <option value="">No filter (analyze everything)</option>
54 <option value="-hom">Analyze homozygous sequence changes only </option>
55 <option value="-het">Analyze heterozygous sequence changes only </option>
56 </param>
57
58 <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
59 <option value="">No filter (analyze everything)</option>
60 <option value="-del">Analyze deletions only </option>
61 <option value="-ins">Analyze insertions only </option>
62 <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>
63 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
64 </param>
65
66 <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">
67 <option value="None" selected="true">None</option>
68 <option value="downstream">Do not show DOWNSTREAM changes </option>
69 <option value="intergenic">Do not show INTERGENIC changes </option>
70 <option value="intron">Do not show INTRON changes </option>
71 <option value="upstream">Do not show UPSTREAM changes </option>
72 <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
73 </param>
74
75 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
76 <option value="">Use default (based on input type)</option>
77 <option value="-0">Force zero-based positions (both input and output)</option>
78 <option value="-1">Force one-based positions (both input and output)</option>
79 </param>
80 </inputs>
81 <outputs>
82 <data format="tabular" name="output" >
83 <change_format>
84 <when input="outputFormat" value="txt" format="tabular" />
85 <when input="outputFormat" value="vcf" format="vcf" />
86 <when input="outputFormat" value="bed" format="bed" />
87 <when input="outputFormat" value="bedAnn" format="bed" />
88 </change_format>
89 </data>
90 <data format="html" name="statsFile" />
91 </outputs>
92 <stdio>
93 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
94 <exit_code range="1:" level="fatal" description="Error" />
95 </stdio>
96 <help>
97
98 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
99
100 For details about this tool, please go to http://snpEff.sourceforge.net
101
102 </help>
103 </tool>
104