<tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01">
  <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 '$input_pairs' pairs.tabix &&
    #if str( $input_pairs.metadata.tabix_index ) != "None":
      ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
    #else:
      tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix &&
    #end if
    cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output'
    ]]>
  </command>
  <inputs>
    <param name="input_pairs" multiple="false"  type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/>
    <section name="pairs_advanced" title="If your input is not already indexed" expanded="False">
      <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>
    </section>
    <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>
    <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 $input_pairs.name and $input_bed.name"/>
  </outputs>
  
  <tests>
    <!-- For the moment I cannot test this tool -->
    <!-- <test>
      <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/>
      <param name="input_bed" value="chr19.1M.bins"/>
      <param name="assembly" value="chr19"/>
      <section name="pairs_advanced">
        <param name="c1" value="3"/>
        <param name="p1" value="4"/>
      </section>
      <param name="c2" value="7"/>
      <param name="p2" value="8"/>
      <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>