annotate VCF_to_VariantDB.xml @ 0:156964ba18fc draft

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<tool id="VCF_to_DB_rev" name="Send VCF file to the Database" version="0.1.1">
  <description>Reverse processing (on VariantDB server)</description>
  <command interpreter="perl">
    VCF_to_VariantDB.pl
      ## THE GALAXY HOST 
      -H 'http://143.169.238.104/galaxy'
      -R $__root_dir__
      ## input file
      -v $input1
      -V $__app__.security.encode_id( '%s' % $input1.id )
      ## user email, for identification in VariantDB, accounts must match
      -u $__user_email__
      
      ## 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
  
      
  </command>
  <requirements>
	<requirement type="package">tabix</requirement>
  </requirements>
  <inputs>
        <param name="input1" type="data" format="vcf" label="VCF file" help="Unified Genotyper VCF File" />
	<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>
        </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 for Report." />
	  </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>
        </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>
		<!-- Specify other VariantDB instances here -->
	</param>
  </inputs>
  <outputs>
    <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/>
  </outputs>
  <help>

**What it does**

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. 

VariantDB is an flexible portal for filtering and annotating variants. 

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**Input file**

VCF file from the GATK Unified Genotyper. Optional : BAM file for storage in VariantDB and subsequent visualisation in IGV.

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**Outputs**

Text file with some results from the vcf-parser. 

  </help>
</tool>