Mercurial > repos > geert-vandeweyer > vcf_to_variantdb
annotate VCF_to_VariantDB.xml @ 10:d5040a542e9d draft
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| author | geert-vandeweyer |
|---|---|
| date | Tue, 21 Oct 2014 05:11:23 -0400 |
| parents | 3b27cae9b359 |
| children | fb815517e918 |
| rev | line source |
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1 <tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.3"> |
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2 <description></description> |
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3 <expand macro="requirements" /> |
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4 <macros> |
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5 <import>VCF_to_VariantDB_macros.xml</import> |
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6 </macros> |
| 0 | 7 <command interpreter="perl"> |
| 4 | 8 VCF_to_VariantDB.pl |
| 8 | 9 -H "@URL@" |
| 0 | 10 -R $__root_dir__ |
| 11 ## input file | |
| 12 -v $input1 | |
| 13 -V $__app__.security.encode_id( '%s' % $input1.id ) | |
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14 ## user email, for identification in DataBase |
| 0 | 15 -u $__user_email__ |
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3b27cae9b359
New Version. VariantDB checks for Genome Build matching using the Galaxy dbkey variable.
geert-vandeweyer
parents:
8
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changeset
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16 ## source file dbkey ( match against variantdb genome build) |
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3b27cae9b359
New Version. VariantDB checks for Genome Build matching using the Galaxy dbkey variable.
geert-vandeweyer
parents:
8
diff
changeset
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17 -G ${input1.dbkey} |
| 0 | 18 ## OUTPUT FILE |
| 19 -o $output1 | |
| 20 | |
| 21 ## SAMPLE GENDER | |
| 22 #if $samplegender != "undef": | |
| 23 -g $samplegender | |
| 24 #end if | |
| 25 | |
| 26 ## SAMPLE NAME | |
| 27 #if $namefromselect.namesource == "typed" : | |
| 28 #if $namefromselect.typedname != "": | |
| 29 -n "${namefromselect.typedname}" | |
| 30 #end if | |
| 31 #elif $namefromselect.namesource == "other": | |
| 32 -n "${namefromselect.namefile.display_name}" | |
| 33 #elif $namefromselect.namesource == "vcf": | |
| 34 -n "${input1.display_name}" | |
| 35 #end if | |
| 36 | |
| 37 ## DATA FILES | |
| 38 #if $sendData.store == "true": | |
| 39 -b $bamfile | |
| 40 -B ${bamfile.metadata.bam_index} | |
| 41 -c $__app__.security.encode_id( '%s' % $bamfile.id ) | |
| 42 #end if | |
| 43 | |
| 44 ## The server to send results to | |
| 45 -S $server | |
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46 ## The input file format |
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47 -F $format |
| 0 | 48 |
| 49 </command> | |
| 50 <requirements> | |
| 51 <requirement type="package">tabix</requirement> | |
| 52 </requirements> | |
| 53 <inputs> | |
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54 <param name="input1" type="data" format="vcf" label="VCF file" help="Select variant file to import" /> |
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55 <param name="format" type="select" label="VCF Source Application" help="Supported formats are VCF from UnifiedGenotyper, HaplotypeCaller, Mutect and VarScan"> |
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56 <option value="UG">GATK Unified Genotyper</option> |
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57 <option value="HC">GATK Haplotype Caller</option> |
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58 <option value="MT">GATK MuTect</option> |
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59 <option value="VS">Samtools VarScan</option> |
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60 </param> |
| 0 | 61 <conditional name="sendData"> |
| 62 <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." > | |
| 63 <option value="false">No</option> | |
| 64 <option value="true">Yes</option> | |
| 65 </param> | |
| 66 <when value="true"> | |
| 67 <param name="bamfile" type="data" format="bam" label="BAM File." /> | |
| 68 </when> | |
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69 <when value="false" /> |
| 0 | 70 </conditional> |
| 71 | |
| 72 <conditional name="namefromselect"> | |
| 73 <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" > | |
| 74 <option value="typed">Type the samplename</option> | |
| 75 <option value="vcf">Use the VCF File name</option> | |
| 76 <option value="other">Select a file to base the name on</option> | |
| 77 </param> | |
| 78 <when value="typed"> | |
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79 <param name="typedname" type="text" size="25" label="Sample Name." /> |
| 0 | 80 </when> |
| 81 <when value="other"> | |
| 82 <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" /> | |
| 83 </when> | |
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84 <when value="vcf"/> |
| 0 | 85 </conditional> |
| 86 <param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well."> | |
| 87 <option value="undef">Unspecified</option> | |
| 88 <option value="Male">Male</option> | |
| 89 <option value="Female">Female</option> | |
| 90 </param> | |
| 91 <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."> | |
| 92 <option value="http://143.169.238.104/variantdb/">Main Server @ University of Antwerp</option> | |
| 93 </param> | |
| 94 </inputs> | |
| 95 <outputs> | |
| 96 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/> | |
| 97 </outputs> | |
| 98 <help> | |
| 99 | |
| 100 **What it does** | |
| 101 | |
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102 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. |
| 0 | 103 |
| 104 ------ | |
| 105 | |
| 106 | |
| 107 **Input file** | |
| 108 | |
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109 VCF file from the GATK Unified Genotyper. |
| 0 | 110 |
| 111 ------ | |
| 112 | |
| 113 **Outputs** | |
| 114 | |
| 115 Text file with some results from the vcf-parser. | |
| 116 | |
| 117 </help> | |
| 10 | 118 <citations> |
| 119 <citation type="doi">10.1186/s13073-014-0074-6</citation> | |
| 120 </citations> | |
| 0 | 121 </tool> |
| 122 | |
| 123 |