Mercurial > repos > geert-vandeweyer > vcf_to_variantdb

comparison VCF_to_VariantDB.xml @ 7:04e3bba317f4 draft

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Added selection to differentiate in VCF format
author geert-vandeweyer
date Thu, 05 Jun 2014 04:02:28 -0400
parents 7ebc71784e9f
children db44ff975de8
comparison
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6:775372e00f55 7:04e3bba317f4
40 -c $__app__.security.encode_id( '%s' % $bamfile.id ) 40 -c $__app__.security.encode_id( '%s' % $bamfile.id )
41 #end if 41 #end if
42 42
43 ## The server to send results to 43 ## The server to send results to
44 -S $server 44 -S $server
45 45 ## The input file format
46 -F $format
46 47
47 </command> 48 </command>
48 <requirements> 49 <requirements>
49 <requirement type="package">tabix</requirement> 50 <requirement type="package">tabix</requirement>
50 </requirements> 51 </requirements>
51 <inputs> 52 <inputs>
52 <param name="input1" type="data" format="vcf" label="VCF file" help="Unified Genotyper VCF File" /> 53 <param name="input1" type="data" format="vcf" label="VCF file" help="Select variant file to import" />
54 <param name="format" type="select" label="VCF Source Application" help="Supported formats are VCF from UnifiedGenotyper, HaplotypeCaller, Mutect and VarScan">
55 <option value="UG">GATK Unified Genotyper</option>
56 <option value="HC">GATK Haplotype Caller</option>
57 <option value="MT">GATK MuTect</option>
58 <option value="VS">Samtools VarScan</option>
59 </param>
53 <conditional name="sendData"> 60 <conditional name="sendData">
54 <param name="store" type="select" label="Store VCF and BAM Files:" help="This option allows you to send the BAM and VCF files to our storage server for dynamic loading into IGV. If you store them there, please delete them here." > 61 <param name="store" type="select" label="Store VCF and BAM Files:" help="This option allows you to send the BAM and VCF files to our storage server for dynamic loading into IGV. If you store them there, please delete them here." >
55 <option value="false">No</option> 62 <option value="false">No</option>
56 <option value="true">Yes</option> 63 <option value="true">Yes</option>
57 </param> 64 </param>
58 <when value="true"> 65 <when value="true">
59 <param name="bamfile" type="data" format="bam" label="BAM File." /> 66 <param name="bamfile" type="data" format="bam" label="BAM File." />
60 </when> 67 </when>
68 <when value="false" />
61 </conditional> 69 </conditional>
62 70
63 <conditional name="namefromselect"> 71 <conditional name="namefromselect">
64 <param name="namesource" type="select" label="Provide a Sample Name :" help="If no name is specified, a new sample will be created, and you will be notified of the name" > 72 <param name="namesource" type="select" label="Provide a Sample Name :" help="If no name is specified, a new sample will be created, and you will be notified of the name" >
65 <option value="typed">Type the samplename</option> 73 <option value="typed">Type the samplename</option>
70 <param name="typedname" type="text" size="25" label="Sample Name." /> 78 <param name="typedname" type="text" size="25" label="Sample Name." />
71 </when> 79 </when>
72 <when value="other"> 80 <when value="other">
73 <param name="namefile" type="data" format="sam,bam,fastq,fasta,bed,fastqsanger,fastqillumina,txt,vcf" label="Select a file from the history to base the sample name upon" /> 81 <param name="namefile" type="data" format="sam,bam,fastq,fasta,bed,fastqsanger,fastqillumina,txt,vcf" label="Select a file from the history to base the sample name upon" />
74 </when> 82 </when>
83 <when value="vcf"/>
75 </conditional> 84 </conditional>
76 <param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well."> 85 <param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well.">
77 <option value="undef">Unspecified</option> 86 <option value="undef">Unspecified</option>
78 <option value="Male">Male</option> 87 <option value="Male">Male</option>
79 <option value="Female">Female</option> 88 <option value="Female">Female</option>
87 </outputs> 96 </outputs>
88 <help> 97 <help>
89 98
90 **What it does** 99 **What it does**
91 100
92 This tools sends the results from the GATK unified genotyper to a VariantDB server. From there, variants can be compared between samples, filtered on various annotations etc. To add servers, specify them in the tool configuration XML file. 101 This tools sends VCF files with results from the GATK unified genotyper, HaploType Caller, Mutect or samtools VarScan to a VariantDB server. From there, variants can be compared between samples, filtered on various annotations etc. To add servers, specify them in the tool configuration XML file.
93 102
94 ------ 103 ------
95 104
96 105
97 **Input file** 106 **Input file**