<tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy1" profile="22.05">
  <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command detect_errors="exit_code"><![CDATA[
    ##set up input files
    ln -s '$format_sel.input_pairs' pairs.tabix &&
    ln -s '$format_sel.input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
    cooler cload tabix --assembly '$assembly'
    #if $format_sel.format == "juicer_medium":
      -c2 7 -p2 8
    #else:
      -c2 $format_sel.c2 -p2 $format_sel.p2
    #end if
    '$input_bed' pairs.tabix '$output'
    ]]>
  </command>
  <inputs>
    <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">
        <param name="input_pairs" multiple="false"  type="data" format="juicer_medium_tabix.gz" label="Select the output of csort_tabix."/>
      </when>
      <when value="other">
        <param name="input_pairs" multiple="false"  type="data" format="interval_tabix.gz" label="Select the output of csort_tabix."/>
        <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort).">
          <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 (same as in csort).">
          <validator type="in_range" min="1" />
        </param>
      </when>
    </conditional>
    <param name="assembly" type="text" label="name of genome assembly"/>
    <param name="input_bed" multiple="false"  type="data" format="bed" label="Select the output of makebins."/>
  </inputs>
  
  <outputs>
    <data format="cool" name="output" label="cool file from $format_sel.input_pairs.name and $input_bed.name"/>
  </outputs>
  
  <tests>
    <test>
      <conditional name="format_sel">
        <param name="format" value="juicer_medium"/>
        <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/>
      </conditional>
      <param name="input_bed" value="chr19.1M.bins"/>
      <param name="assembly" value="chr19"/>
      <output name="output" file="input.cool" compare="sim_size"/>
    </test>
    <test>
      <conditional name="format_sel">
        <param name="format" value="other"/>
        <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/>
        <param name="c2" value="7"/>
        <param name="p2" value="8"/>
      </conditional>
      <param name="input_bed" value="chr19.1M.bins"/>
      <param name="assembly" value="chr19"/>
      <output name="output" file="input.cool" compare="sim_size"/>
    </test>
  </tests> 

  <help>
    **cooler cload**
    tool developped by mirnylab
    see https://github.com/open2c/cooler
    and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix
        
    command-line::
    
      cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output
    
  </help>
  <expand macro="citation_cooler" />
</tool>