annotate cooler_zoomify.xml @ 0:4069512d96bd draft default tip

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

<tool id="cooler_zoomify" name="Cooler zoomify" version="@VERSION@+galaxy0" profile="18.01">
  <description>Generate a multi-resolution cooler file by coarsening</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <command detect_errors="exit_code"><![CDATA[
    cooler zoomify -p \${GALAXY_SLOTS:-4}
    -c $c
    -r '$r'
    -o '$output'
    '$input'
    ]]>
  </command>
  <inputs>
    <param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to zoomify"/> 
    <param argument="-c" type="integer" value="10000000" label="Number of pixels dedicated to each process"/>
    <param argument="-r" type="text" value="B" label="Resultion" help="Comma-separated list of target resolutions. Use suffixes B or N to specify a progression: B for binary (geometric steps of factor 2), N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5). Examples: 1000B=1000,2000,4000,8000,... 1000N=1000,2000,5000,10000,... 5000N=5000,10000,25000,50000,... 4DN is an alias for 1000,2000,5000N">
        <validator type="regex">[BDN0-9,]+</validator>
        </param>
  </inputs>
  
  <outputs>
    <data format="mcool" name="output" label="Multi-resolution mcool file from $input.name"/>
  </outputs>
  
  <tests>
    <test>
      <param name="input" value="input.cool" ftype="cool"/>
      <output name="output" file="output.mcool" ftype="mcool" compare="sim_size"/>
      <param name="r" value="1000000,2000000,4000000"/>
    </test>
  </tests> 

  <help>
    **cooler zoomify**
    Generate a multi-resolution cooler file by coarsening
    Given a set of resolutions, generate a multi-cooler file from a cooler for visualisation with higlass.
  </help>
  <expand macro="citation_cooler" />
</tool>