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comparison gemini_load.xml @ 0:720cbfb4190d draft

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Imported from capsule None
author iuc
date Mon, 25 Aug 2014 17:15:54 -0400
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children 93bb0cfacefb
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-1:000000000000 0:720cbfb4190d
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Loading a VCF file into GEMINI</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">load</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini
12 --annotation-dir ${annotation_databases.fields.path}
13 @BINARY@
14 -v "${ infile }"
15 -t $annotation_type
16
17 #if $ped:
18 -p $ped
19 #end if
20
21 $skip_gerp_bp
22 $skip_cadd
23 $skip_gene_tables
24 $no_load_genotypes
25 $no_genotypes
26 $passonly
27 --cores \${GALAXY_SLOTS:-4}
28
29 "${ outfile }"
30 ]]>
31 </command>
32 <expand macro="stdio" />
33 <inputs>
34 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" />
35
36 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
37 <option value="snpEff">snpEff annotated VCF file</option>
38 <option value="VEP">VEP annotated VCF file</option>
39 </param>
40 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
41 <expand macro="annotation_dir" />
42
43 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
44 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
45
46 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
47 label="Do not load CADD scores" help="(--skip-cadd)"/>
48
49 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
50 label="Do not load gene tables" help="(--skip-gene-tables)"/>
51
52 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
53 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
54
55 <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
56 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
57
58 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
59 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
60
61 </inputs>
62 <outputs>
63 <data name="outfile" format="sqlite" label="${tool.name} on ${on_string}" />
64 </outputs>
65 <tests>
66 <test>
67 </test>
68 </tests>
69 <help>
70 **What it does**
71
72 Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework.
73 We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff.
74
75 http://gemini.readthedocs.org/en/latest/content/loading.html
76
77 @CITATION@
78 </help>
79 <expand macro="citations"/>
80 </tool>