annotate cooler_csort_tabix.xml @ 4:026950a1853c draft default tip

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit bee0809b51b16e750353b19fad34bfcf5e93ab13

<tool id="cooler_csort_tabix" name="cooler csort with tabix" version="@VERSION@+galaxy1" profile="22.05">
  <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 
    #if str($format_sel.format) == "juicer_medium":
      -c1 3 -c2 7 -p1 4 -p2 8
    #else:
      -c1 $format_sel.c1 -c2 $format_sel.c2 -p1 $format_sel.p1 -p2 $format_sel.p2
    #end if
    -o '$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)."/>
    <conditional name="format_sel">
        <param name="format" type="select" label="Format of your input file">
            <option value="juicer_medium">Juicer Medium Format</option>
            <option value="other">Other</option>
        </param>
        <when value="juicer_medium"/>
        <when value="other">
          <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>
        </when>
    </conditional>
    <expand macro="size_macro" />
  </inputs>
  
  <outputs>
    <data format="interval_tabix.gz" name="output" label="sorted and indexed contact list of $input.name">
      <actions>
        <conditional name="format_sel.format">
          <when value="juicer_medium">
            <action type="format" default="juicer_medium_tabix.gz" />
          </when>
          <when value="other">
            <action type="metadata" name="chromCol" default="$format_sel.c1"/>
            <action type="metadata" name="startCol" default="$format_sel.p1"/>
            <action type="metadata" name="endCol" default="$format_sel.p1"/>
          </when>
         </conditional>
      </actions>
    </data>
  </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>
      <conditional name="format_sel">
        <param name="format" value="juicer_medium"/>
      </conditional>
      <output name="output" file="input.validPairs.tabix" decompress="true">
        <metadata name="chromCol" value="3" />
        <metadata name="startCol" value="4" />
        <metadata name="endCol" value="4" />
      </output>
    </test>
    <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>
      <conditional name="format_sel">
        <param name="format" value="other"/>
        <param name="c1" value="3"/>
        <param name="p1" value="4"/>
        <param name="c2" value="7"/>
        <param name="p2" value="8"/>
      </conditional>
      <output name="output" file="input.validPairs.tabix" decompress="true">
        <metadata name="chromCol" value="3" />
        <metadata name="startCol" value="4" />
        <metadata name="endCol" value="4" />
      </output>
    </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>