Mercurial > repos > geert-vandeweyer > vcf_to_variantdb
annotate VCF_to_VariantDB.xml @ 7:04e3bba317f4 draft
Added selection to differentiate in VCF format
| author | geert-vandeweyer |
|---|---|
| date | Thu, 05 Jun 2014 04:02:28 -0400 |
| parents | 7ebc71784e9f |
| children | db44ff975de8 |
| rev | line source |
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1 <tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.2"> |
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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 |
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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__ |
| 16 | |
| 17 ## OUTPUT FILE | |
| 18 -o $output1 | |
| 19 | |
| 20 ## SAMPLE GENDER | |
| 21 #if $samplegender != "undef": | |
| 22 -g $samplegender | |
| 23 #end if | |
| 24 | |
| 25 ## SAMPLE NAME | |
| 26 #if $namefromselect.namesource == "typed" : | |
| 27 #if $namefromselect.typedname != "": | |
| 28 -n "${namefromselect.typedname}" | |
| 29 #end if | |
| 30 #elif $namefromselect.namesource == "other": | |
| 31 -n "${namefromselect.namefile.display_name}" | |
| 32 #elif $namefromselect.namesource == "vcf": | |
| 33 -n "${input1.display_name}" | |
| 34 #end if | |
| 35 | |
| 36 ## DATA FILES | |
| 37 #if $sendData.store == "true": | |
| 38 -b $bamfile | |
| 39 -B ${bamfile.metadata.bam_index} | |
| 40 -c $__app__.security.encode_id( '%s' % $bamfile.id ) | |
| 41 #end if | |
| 42 | |
| 43 ## The server to send results to | |
| 44 -S $server | |
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45 ## The input file format |
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46 -F $format |
| 0 | 47 |
| 48 </command> | |
| 49 <requirements> | |
| 50 <requirement type="package">tabix</requirement> | |
| 51 </requirements> | |
| 52 <inputs> | |
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53 <param name="input1" type="data" format="vcf" label="VCF file" help="Select variant file to import" /> |
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geert-vandeweyer
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54 <param name="format" type="select" label="VCF Source Application" help="Supported formats are VCF from UnifiedGenotyper, HaplotypeCaller, Mutect and VarScan"> |
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55 <option value="UG">GATK Unified Genotyper</option> |
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56 <option value="HC">GATK Haplotype Caller</option> |
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57 <option value="MT">GATK MuTect</option> |
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58 <option value="VS">Samtools VarScan</option> |
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04e3bba317f4
Added selection to differentiate in VCF format
geert-vandeweyer
parents:
4
diff
changeset
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59 </param> |
| 0 | 60 <conditional name="sendData"> |
| 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." > | |
| 62 <option value="false">No</option> | |
| 63 <option value="true">Yes</option> | |
| 64 </param> | |
| 65 <when value="true"> | |
| 66 <param name="bamfile" type="data" format="bam" label="BAM File." /> | |
| 67 </when> | |
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04e3bba317f4
Added selection to differentiate in VCF format
geert-vandeweyer
parents:
4
diff
changeset
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68 <when value="false" /> |
| 0 | 69 </conditional> |
| 70 | |
| 71 <conditional name="namefromselect"> | |
| 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" > | |
| 73 <option value="typed">Type the samplename</option> | |
| 74 <option value="vcf">Use the VCF File name</option> | |
| 75 <option value="other">Select a file to base the name on</option> | |
| 76 </param> | |
| 77 <when value="typed"> | |
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2
d03a63a57e82
New version, better following configuration guidelines
geert-vandeweyer
parents:
0
diff
changeset
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78 <param name="typedname" type="text" size="25" label="Sample Name." /> |
| 0 | 79 </when> |
| 80 <when value="other"> | |
| 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" /> | |
| 82 </when> | |
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7
04e3bba317f4
Added selection to differentiate in VCF format
geert-vandeweyer
parents:
4
diff
changeset
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83 <when value="vcf"/> |
| 0 | 84 </conditional> |
| 85 <param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well."> | |
| 86 <option value="undef">Unspecified</option> | |
| 87 <option value="Male">Male</option> | |
| 88 <option value="Female">Female</option> | |
| 89 </param> | |
| 90 <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."> | |
| 91 <option value="http://143.169.238.104/variantdb/">Main Server @ University of Antwerp</option> | |
| 92 </param> | |
| 93 </inputs> | |
| 94 <outputs> | |
| 95 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/> | |
| 96 </outputs> | |
| 97 <help> | |
| 98 | |
| 99 **What it does** | |
| 100 | |
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7
04e3bba317f4
Added selection to differentiate in VCF format
geert-vandeweyer
parents:
4
diff
changeset
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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. |
| 0 | 102 |
| 103 ------ | |
| 104 | |
| 105 | |
| 106 **Input file** | |
| 107 | |
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2
d03a63a57e82
New version, better following configuration guidelines
geert-vandeweyer
parents:
0
diff
changeset
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108 VCF file from the GATK Unified Genotyper. |
| 0 | 109 |
| 110 ------ | |
| 111 | |
| 112 **Outputs** | |
| 113 | |
| 114 Text file with some results from the vcf-parser. | |
| 115 | |
| 116 </help> | |
| 117 </tool> | |
| 118 | |
| 119 |