view cooler_csort_tabix.xml @ 0:36d7d522f13e draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296

<tool id="cooler_csort_tabix" name="cooler csort with tabix" version="@VERSION@+galaxy0" profile="18.01">
  <description> Sort and index a contact list.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command detect_errors="exit_code"><![CDATA[
    cooler csort -i tabix -c1 $c1 -c2 $c2 -p1 $p1 -p2 $p2 -o '$output' '$input'
    #if str($size_source.size_source_selector) == 'history':
      '$size_source.chromosomeSize'
    #else:
      '$size_source.fasta_cached.fields.path'.fai
    #end if
  ]]>
  </command>
  <inputs>
    <param name="input" multiple="false"  type="data" format="tabular" label="Select a file with the coordinates of the pairs (minimum 4 columns with chromosome and position for each mate)."/>
    <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1.">
      <validator type="in_range" min="1" />
    </param>
    <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1.">
      <validator type="in_range" min="1" />
    </param>
    <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2.">
      <validator type="in_range" min="1" />
    </param>
    <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2.">
      <validator type="in_range" min="1" />
    </param>
    <expand macro="size_macro" />
  </inputs>
  
  <outputs>
    <data format="tabix" name="output" label="sorted and indexed contact list of $input.name"/>
  </outputs>
  
  <tests>
    <test>
      <param name="input" value="input.validPairs.txt"/>
      <conditional name="size_source">
        <param name="size_source_selector" value="history"/>
        <param name="chromosomeSize" value="chr19.size"/>
      </conditional>
      <param name="c1" value="3"/>
      <param name="p1" value="4"/>
      <param name="c2" value="7"/>
      <param name="p2" value="8"/>
      <output name="output" file="input.validPairs.tabix" decompress="true"/>
    </test>
  </tests> 

  <help>
    **cooler csort**
    tool developped by mirnylab
    see https://github.com/open2c/cooler
    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-csort
    
    command-line::

      cooler csort -i tabix -c1 c1 -c2 c2 -p1 p1 -p2 p2 -o output input chromosomeSize
    
  </help>
  <expand macro="citation_cooler" />
</tool>