comparison filter-density.xml @ 1:c9a43abcd993 draft default tip

"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"

0:c27b4346352f

<tool id="filterdensity" name="Filter Density" version ="1.8.2">
  <description>Identify high density positions within indvidual genomes</description>
  <requirements>
    <requirement type="package" version="1.8.2">snvphyl-tools</requirement>
  </requirements>
  <command detect_errors="exit_code">
      bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out
      #if $window_size:
      --window_size $window_size
      #end if

      --threshold $threshold
      #end if
  </command>
  <inputs>
    <param name="vcf" type="data" label="Input vcf file" format="vcf" />
    <param name="window_size" type="integer" label="Size of search window" format="" optional="true"/>
    <param name="threshold"  type="integer" label="Density threshold cutoff" format="" optional="true"/>
  </inputs>
  <outputs>
    <data format="txt" name="out" label="High density regions"/>
    <data format="bcf" name="filtered_bcf"/>
  </outputs>

**Parameters**
  - vcf - A vcf file to be analyzed for SNV density.
  - threshold - The threshold distance between SNV's in order for them to be considered 'high density'
  - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density.
  </help>

  <citations>
  </citations>

</tool>

1:c9a43abcd993

<tool id="filterdensity" name="Filter Density" version ="@VERSION@+galaxy1">
  <description>Identify high density positions within indvidual genomes</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code">
      bcftools plugin filter_snv_density $vcf -O b -o $filtered_bcf -- --filename $vcf --region_file $out
      #if $window_size:
      --window_size $window_size
      #end if

      --threshold $threshold
      #end if
  </command>
  <inputs>
    <param name="vcf" type="data" label="Input vcf file" format="vcf" />
    <param name="window_size" type="integer" min="1" label="Size of search window" format="" optional="true"/>
    <param name="threshold"  type="integer"  min="1" label="Density threshold cutoff" format="" optional="true"/>
  </inputs>
  <outputs>
    <data format="txt" name="out" label="High density regions"/>
    <data format="bcf" name="filtered_bcf"/>
  </outputs>

**Parameters**
  - vcf - A vcf file to be analyzed for SNV density.
  - threshold - The threshold distance between SNV's in order for them to be considered 'high density'
  - window_size - The size of the window, in base pairs, that will be looked at at any given time to calculate density.
  </help>
  <expand macro="citations"/>
</tool>