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comparison snpSift_geneSets.xml @ 5:d12a810c837e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:57 -0400
parents 847db7b39bdc
children
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4:ea2e7d299365 5:d12a810c837e
1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.1"> 1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0">
2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description> 2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros> 6 <macros>
7 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 @CONDA_SNPSIFT_JAR_PATH@ && 13 SnpSift -Xmx2G geneSets -v
14 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" geneSets -v 14 #if $db_opts.db_opts_selector == 'db'
15 #if $db_opts.db_opts_selector == "db" 15 '${db_opts.database.fields.path}'
16 "${db_opts.database.fields.path}" 16 #elif $db_opts.db_opts_selector == 'histdb'
17 #elif $db_opts.db_opts_selector == "histdb" 17 '$db_opts.histdb'
18 "$db_opts.histdb" 18 #end if
19 #end if 19 '$input'
20 "$input" 2> "$log" > "$output" 20 2> '$log'
21 ]]> 21 > '$output'
22 </command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 24 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
25 <conditional name="db_opts"> 25 <conditional name="db_opts">
26 <param name="db_opts_selector" type="select" label="Select Annotation database" help=""> 26 <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
27 <option value="db" selected="True">Locally installed database</option> 27 <option value="db" selected="True">Locally installed database</option>
28 <option value="histdb">database from your history</option> 28 <option value="histdb">database from your history</option>
29 </param> 29 </param>
30 <when value="db"> 30 <when value="db">
31 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)"> 31 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
32 <options from_data_table="snpeff_msigdb_database" /> 32 <options from_data_table="snpeff_msigdb_database" />
33 </param> 33 </param>
37 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" /> 37 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
38 </when> 38 </when>
39 </conditional> 39 </conditional>
40 </inputs> 40 </inputs>
41 <outputs> 41 <outputs>
42 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> 42 <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" />
43 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> 43 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
44 </outputs> 44 </outputs>
45 <tests> 45 <tests>
46 </tests> 46 </tests>
47 <help><![CDATA[ 47 <help><![CDATA[
48 This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome. 48 This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome.
54 The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects. 54 The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects.
55 55
56 @EXTERNAL_DOCUMENTATION@ 56 @EXTERNAL_DOCUMENTATION@
57 57
58 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ 58 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
59 ]]> 59 ]]></help>
60 </help>
61 <expand macro="citations"> 60 <expand macro="citations">
62 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation --> 61 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
63 </expand> 62 </expand>
64 </tool> 63 </tool>