view covacs_ApplyRecalibrator.xml @ 0:c785cec34cdc draft

Uploaded

 <tool id="covacs_ApplyRecalibrator" name="covacs_ApplyRecalibrator" version="3.8">
  <description>gatk ApplyRecalibrator wrapper </description>
  <macros>
	<import>bed_macros.xml</import>
  </macros>
  <requirements>
  	<requirement type="package" version="3.8" >gatk</requirement>
  </requirements>
  <command>
    <![CDATA[
	 ### call the .sh to untar the package 
        sh $__tool_directory__/mv_untar_gatk.sh &&	


	
	#if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
	 ln -s $bed_source.bed_history region.bed &&
	#end if

	 ln -s $input1 input1.vcf &&

	java  -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -T ApplyRecalibration
	


	#if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
        -L  region.bed
        #end if
        #if $bed_source.bed_source_selector == "cached"
        -L $bed_source.bed_cached.fields.path
        #end if


	-ip $ip
	###index from .loc
	-R $ref_file.fields.path

	-input input1.vcf
	--ts_filter_level $ts_filter_level
	-tranchesFile $input2
	-recalFile $input3
	-mode $mode
	-ef -o variants_recal.filtered.98HQ.vcf 2> $log




	]]>
  </command>
  <inputs>
    <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
       <options from_data_table="covacs_gatk_indexes">
         <filter type="sort_by" column="2" />
         <validator type="no_options" message="No indexes are available" />
       </options>
       <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
    </param>
    <param format="vcf" name="input1" label="input vcf" type="data" optional="true" />
    <expand macro="bed_loc"/>
    <param name="ip" type="integer" value="100" help="Amount of padding (in bp) to add to each interval"/>
    <param name="ts_filter_level" type="float" value="99.5" help="The truth sensitivity level at which to start filtering"/>
    <param name="input2" type="data" label="tranchesfile" help="tranches file from VariantRecalibrator"/>
    <param name="input3" type="data" label="recalfile" help="tranches file from VariantRecalibrator"/>
    <param name="mode" type="select" help="Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels">
	<option value="SNP">snp</option>
	<option value="INDEL">INDEL</option>
    </param>
  </inputs>
  <outputs>
    <data format="vcf" name="variants_recal" from_work_dir="variants_recal.filtered.98HQ.vcf" label="${tool.name} on ${on_string}:recal_filtered"/>
    <data format="txt" name="log"  label="${tool.name} on ${on_string}:log"/>
  </outputs>
  <help>
.. class:: warningmark

**IMPORTANT** to get the wrapper ready to start the admin user have to download gatk GATK version 3.8 from the broadinstitute site https://software.broadinstitute.org/gatk/download/archive and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file

		**more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_ApplyRecalibration.php

-----

**implemented options** ApplyRecalibrator:

**-L**                  : One or more genomic intervals over which to operate(file.bed)

**-ip**                 : Amount of padding (in bp) to add to each interval

**-R**                  : Reference sequence file

**-ts\_filter_\level**    : The truth sensitivity level at which to start filtering

**-tranchesFile**       : Level of sensitivity. A tranchesfile is required. Please read the GATK manual if you do according to the input tranches file

**-recallFile**         : The input recal file used by ApplyRecalibration

**-mode**               : Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels

  </help>
  <citations>
        <citation type="doi">10.1186/s12864-018-4508-1</citation>
  </citations>
</tool>