annotate consolidate_vcfs.xml @ 0:b42c82186e85 draft

"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"

<tool id="consolidate_vcfs" name="Consolidate VCFs" version ="1.8.2">
  <description>combine freebayes and mpileup files for use by vcf2snvalignment</description>
    <requirements>
      <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
    </requirements>
  <command detect_errors="exit_code"><![CDATA[

        #set $name = str($freebayes).split('/')[-1]
         ln -f -s $freebayes &&

        #if $freebayes.metadata.bcf_index:
          ln -s '${$freebayes.metadata.bcf_index}' ${name}.csi &&
        #else
	  bcftools index $name &&
	#end if


        #set $name = str($mpileup).split('/')[-1]
         ln -f -s $mpileup &&

        #if $mpileup.metadata.bcf_index:
          ln -s '${$mpileup.metadata.bcf_index}' ${name}.csi &&
        #else
	  bcftools index $name &&
	#end if

        consolidate_vcfs.pl


        -c "$coverage"
      	--min-mean-mapping "$mean_mapping"
      	--snv-abundance-ratio "$snv_abundance_ratio"

        #set $path = str($freebayes).split('/')[-1]
        --vcfsplit "$path"

        #set $path = str($mpileup).split('/')[-1]
        --mpileup "$path"

        #set $path = str($path).split('/')[-1]
        #if $filtered_density:
          --filtered-density-out "$filtered_density"
        #end if

        #if $use_density_filter.select_list == "no":
          --skip-density-filter
        #else
          #if $use_density_filter.window_size:
            --window-size "$use_density_filter.window_size"
          #end if
          #if $use_density_filter.threshold:
            --density-threshold "$use_density_filter.threshold"
          #end if
        #end if

        ##mark where the output files will be sent to, simply have to match them up later in the xml output section
        -o $bcf_combined
  ]]>
  </command>
  <inputs>
    <param name="coverage" type="integer" value="15" label="Minimum coverage"/>
    <param name="mean_mapping" type="integer" value="30" label="Minimum mean mapping quality"/>
    <param name="snv_abundance_ratio" type="text" value="0.75" optional="false" label="SNV abundance ratio"/>
    <param name="freebayes" type="data" label="FreeBayes filtered BCF" help="" optional="false" format="bcf_bgzip,bcf" />
    <param name="mpileup" type="data" label="Mpileup BCF" help="" optional="false" format="bcf_bgzip,bcf" />
    <conditional name="use_density_filter">
      <param name="select_list" type="select" label= "SNV density filtering">
        <option value="yes">Apply</option>
        <option value="no">Don't apply</option>
      </param>
      <when value="yes">
        <param name="window_size" type="integer" label="Size of search window" format="" optional="false" value="100"/>
        <param name="threshold"  type="integer" label="Density threshold cutoff" format="" optional="false" value="10"/>
      </when>
      <when value="no">
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="bcf_bgzip" name="bcf_combined"/>
    <data format="txt" name="filtered_density" label="High density regions"/>
  </outputs>
  <tests>
    <test>
      <param name="coverage" value="5"/>
      <param name="freebayes" value="freebayes/v1.bcf" />
      <param name="mpileup" value="mpileup/v1.bcf" />
      <param name="mean_mapping" value="30" />
      <param name="snv_abundance_ratio" value="0.75" />
      <param name="window_size" value="500" />
      <param name="threshold" value="2" />
      <output name="bcf_combined" file="v1.bcf.gz" compare="sim_size" delta="500"/>
      <output name="filtered_density" file="expected_regions.txt"/>
    </test>
    <test>
      <param name="coverage" value="5"/>
      <param name="freebayes" value="freebayes/v2.bcf" />
      <param name="mpileup" value="mpileup/v2.bcf" />
      <param name="mean_mapping" value="30" />
      <param name="snv_abundance_ratio" value="0.75" />
      <param name="window_size" value="500" />
      <param name="threshold" value="2" />
      <output name="bcf_combined" file="v2.bcf.gz" compare="sim_size" delta="500"/>
      <output name="filtered_density" file="expected_regions.txt"/>
    </test>
  </tests>

  <help>
  Merges variant and non-variant calls (in VCF format) produced from two independent base callers, FreeBayes, and SAMtools/BCFtools. Produces a merged set of high-quality variant and non-variant calls (in BCF format).  Optionally, produces a list of SNV-dense regions above the passed thresholds.
  </help>

  <citations>
  </citations>

</tool>