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comparison gemini_load.xml @ 17:65f742e605ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 9876fc2456ac
children
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16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Loading a VCF file into GEMINI</description> 2 <description>Loading a VCF file into GEMINI</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">load</token> 5 <token name="@BINARY@">load</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 ln -s "${ infile }" input.vcf && 12 ln -s "${ infile }" input.vcf &&
12 13
13 gemini 14 gemini
14 --annotation-dir ${annotation_databases.fields.path} 15 --annotation-dir ${annotation_databases.fields.path}
15 @BINARY@ 16 @BINARY@
16 -v input.vcf 17 -v input.vcf
17 #if str( $annotation_type ) != "None": 18 #if str( $annotation_type ) != "None":
18 -t $annotation_type 19 -t $annotation_type
31 --cores \${GALAXY_SLOTS:-4} 32 --cores \${GALAXY_SLOTS:-4}
32 33
33 "${ outfile }" 34 "${ outfile }"
34 ]]> 35 ]]>
35 </command> 36 </command>
36 <expand macro="stdio" />
37 <inputs> 37 <inputs>
38 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported."> 38 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported.">
39 <options> 39 <options>
40 <filter type="add_value" value="hg19" /> 40 <filter type="add_value" value="hg19" />
41 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" /> 41 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
49 <option value="VEP">VEP annotated VCF file</option> 49 <option value="VEP">VEP annotated VCF file</option>
50 </param> 50 </param>
51 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" /> 51 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
52 <expand macro="annotation_dir" /> 52 <expand macro="annotation_dir" />
53 53
54 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False" 54 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
55 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/> 55 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
56 56
57 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False" 57 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
58 label="Do not load CADD scores" help="(--skip-cadd)"/> 58 label="Do not load CADD scores" help="(--skip-cadd)"/>
59 59
60 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False" 60 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
61 label="Do not load gene tables" help="(--skip-gene-tables)"/> 61 label="Do not load gene tables" help="(--skip-gene-tables)"/>
62 62
63 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" 63 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
64 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/> 64 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
65 65
66 <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False" 66 <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
67 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/> 67 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
68 68
69 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False" 69 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
70 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/> 70 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
71 71
72 </inputs> 72 </inputs>
73 <outputs> 73 <outputs>
74 <data name="outfile" format="gemini.sqlite" /> 74 <data name="outfile" format="gemini.sqlite" />