annotate VCF_to_VariantDB.xml @ 10:d5040a542e9d draft

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<tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.3">
  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>VCF_to_VariantDB_macros.xml</import>
  </macros>
  <command interpreter="perl">
    VCF_to_VariantDB.pl
      -H "@URL@"
      -R $__root_dir__
      ## input file
      -v $input1
      -V $__app__.security.encode_id( '%s' % $input1.id )
      ## user email, for identification in DataBase
      -u $__user_email__
      ## source file dbkey ( match against variantdb genome build)
      -G ${input1.dbkey} 
      ## OUTPUT FILE 
	-o $output1

      ## SAMPLE GENDER
      #if $samplegender != "undef":
	-g $samplegender
      #end if

      ## SAMPLE NAME 
      #if $namefromselect.namesource == "typed" :
	#if $namefromselect.typedname != "":
          -n "${namefromselect.typedname}"
	#end if
      #elif $namefromselect.namesource == "other":
          -n "${namefromselect.namefile.display_name}"
      #elif $namefromselect.namesource == "vcf":
	  -n "${input1.display_name}"
      #end if

      ## DATA FILES 
      #if $sendData.store == "true":
	  -b $bamfile
	  -B ${bamfile.metadata.bam_index}
	  -c $__app__.security.encode_id( '%s' % $bamfile.id )
      #end if

      ## The server to send results to
	-S $server
      ## The input file format
	-F $format 
      
  </command>
  <requirements>
	<requirement type="package">tabix</requirement>
  </requirements>
  <inputs>
        <param name="input1" type="data" format="vcf" label="VCF file" help="Select variant file to import" />
	<param name="format" type="select" label="VCF Source Application" help="Supported formats are VCF from UnifiedGenotyper, HaplotypeCaller, Mutect and VarScan">
		<option value="UG">GATK Unified Genotyper</option>
		<option value="HC">GATK Haplotype Caller</option>
		<option value="MT">GATK MuTect</option>
		<option value="VS">Samtools VarScan</option>
	</param>
	<conditional name="sendData">
	  <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." >
		<option value="false">No</option>
		<option value="true">Yes</option>
	  </param>
 	  <when value="true">
		<param name="bamfile" type="data" format="bam" label="BAM File." />
	  </when>
	  <when value="false" />
        </conditional>

	<conditional name="namefromselect">
	  <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" >
		<option value="typed">Type the samplename</option>
		<option value="vcf">Use the VCF File name</option>
		<option value="other">Select a file to base the name on</option>
	  </param>
 	  <when value="typed">
		<param name="typedname" type="text" size="25" label="Sample Name." />
	  </when>
	  <when value="other">
		<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" />
	  </when>
	  <when value="vcf"/>
        </conditional>
	<param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well.">
		<option value="undef">Unspecified</option>
		<option value="Male">Male</option>
		<option value="Female">Female</option>
	</param>
	<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.">
		<option value="http://143.169.238.104/variantdb/">Main Server @ University of Antwerp</option>
	</param>
  </inputs>
  <outputs>
    <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/>
  </outputs>
  <help>

**What it does**

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. 

------


**Input file**

VCF file from the GATK Unified Genotyper.

------

**Outputs**

Text file with some results from the vcf-parser. 

  </help>
  <citations>
	<citation type="doi">10.1186/s13073-014-0074-6</citation>
  </citations>
</tool>