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comparison gemini_load.xml @ 2:93bb0cfacefb draft

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author iuc
date Mon, 12 Jan 2015 15:31:50 -0500
parents 720cbfb4190d
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1:d3c4d0208bb2 2:93bb0cfacefb
10 <![CDATA[ 10 <![CDATA[
11 gemini 11 gemini
12 --annotation-dir ${annotation_databases.fields.path} 12 --annotation-dir ${annotation_databases.fields.path}
13 @BINARY@ 13 @BINARY@
14 -v "${ infile }" 14 -v "${ infile }"
15 -t $annotation_type 15 #if str( $annotation_type ) != "None":
16 -t $annotation_type
17 #end if
16 18
17 #if $ped: 19 #if $ped:
18 -p $ped 20 -p $ped
19 #end if 21 #end if
20 22
32 <expand macro="stdio" /> 34 <expand macro="stdio" />
33 <inputs> 35 <inputs>
34 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" /> 36 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" />
35 37
36 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)"> 38 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
37 <option value="snpEff">snpEff annotated VCF file</option> 39 <option value="None">None (not recommended)</option>
40 <option value="snpEff" selected="True">snpEff annotated VCF file</option>
38 <option value="VEP">VEP annotated VCF file</option> 41 <option value="VEP">VEP annotated VCF file</option>
39 </param> 42 </param>
40 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" /> 43 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
41 <expand macro="annotation_dir" /> 44 <expand macro="annotation_dir" />
42 45
58 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False" 61 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
59 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/> 62 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
60 63
61 </inputs> 64 </inputs>
62 <outputs> 65 <outputs>
63 <data name="outfile" format="sqlite" label="${tool.name} on ${on_string}" /> 66 <data name="outfile" format="gemini.sqlite" />
64 </outputs> 67 </outputs>
65 <tests> 68 <tests>
66 <test> 69 <test>
67 </test> 70 </test>
68 </tests> 71 </tests>