Mercurial > repos > geert-vandeweyer > vcf_to_variantdb

comparison VCF_to_VariantDB.xml @ 2:d03a63a57e82 draft

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New version, better following configuration guidelines
author geert-vandeweyer
date Wed, 19 Feb 2014 06:45:32 -0500
parents 156964ba18fc
children 7ebc71784e9f
comparison
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1:355e491dbd0f 2:d03a63a57e82
1 <tool id="VCF_to_DB_rev" name="Send VCF file to the Database" version="0.1.1"> 1 <tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.2">
2 <description>Reverse processing (on VariantDB server)</description> 2 <description></description>
3 <expand macro="requirements" />
4 <macros>
5 <import>VCF_to_VariantDB_macros.xml</import>
6 </macros>
3 <command interpreter="perl"> 7 <command interpreter="perl">
4 VCF_to_VariantDB.pl 8 VCF_to_DB_reverse.pl
5 ## THE GALAXY HOST 9 -H '@URL@'
6 -H 'http://143.169.238.104/galaxy'
7 -R $__root_dir__ 10 -R $__root_dir__
8 ## input file 11 ## input file
9 -v $input1 12 -v $input1
10 -V $__app__.security.encode_id( '%s' % $input1.id ) 13 -V $__app__.security.encode_id( '%s' % $input1.id )
11 ## user email, for identification in VariantDB, accounts must match 14 ## user email, for identification in DataBase
12 -u $__user_email__ 15 -u $__user_email__
13 16
14 ## OUTPUT FILE 17 ## OUTPUT FILE
15 -o $output1 18 -o $output1
16 19
62 <option value="typed">Type the samplename</option> 65 <option value="typed">Type the samplename</option>
63 <option value="vcf">Use the VCF File name</option> 66 <option value="vcf">Use the VCF File name</option>
64 <option value="other">Select a file to base the name on</option> 67 <option value="other">Select a file to base the name on</option>
65 </param> 68 </param>
66 <when value="typed"> 69 <when value="typed">
67 <param name="typedname" type="text" size="25" label="Sample Name for Report." /> 70 <param name="typedname" type="text" size="25" label="Sample Name." />
68 </when> 71 </when>
69 <when value="other"> 72 <when value="other">
70 <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" /> 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" />
71 </when> 74 </when>
72 </conditional> 75 </conditional>
75 <option value="Male">Male</option> 78 <option value="Male">Male</option>
76 <option value="Female">Female</option> 79 <option value="Female">Female</option>
77 </param> 80 </param>
78 <param name="server" type="select" label="VariantDB-Server: " help="Specify the VariantDB server you wish to send the data to. You MUST have a valid account on the target server, identical to your account here."> 81 <param name="server" type="select" label="VariantDB-Server: " help="Specify the VariantDB server you wish to send the data to. You MUST have a valid account on the target server, identical to your account here.">
79 <option value="http://143.169.238.104/variantdb/">Main Server @ University of Antwerp</option> 82 <option value="http://143.169.238.104/variantdb/">Main Server @ University of Antwerp</option>
80 <!-- Specify other VariantDB instances here -->
81 </param> 83 </param>
82 </inputs> 84 </inputs>
83 <outputs> 85 <outputs>
84 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/> 86 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/>
85 </outputs> 87 </outputs>
86 <help> 88 <help>
87 89
88 **What it does** 90 **What it does**
89 91
90 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. Accounts must match between the chosen VariantDB and Galaxy user. 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.
91
92 VariantDB is an flexible portal for filtering and annotating variants.
93 93
94 ------ 94 ------
95 95
96 96
97 **Input file** 97 **Input file**
98 98
99 VCF file from the GATK Unified Genotyper. Optional : BAM file for storage in VariantDB and subsequent visualisation in IGV. 99 VCF file from the GATK Unified Genotyper.
100 100
101 ------ 101 ------
102 102
103 **Outputs** 103 **Outputs**
104 104