annotate macros.xml @ 2:8f9fe0667b89 draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 060279258b63713bcfa4f67c0a3cee75d32a7266

<macros>
  <token name="@VERSION@">0.9.3</token>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.18">htslib</requirement>
      <requirement type="package" version="@VERSION@">cooler</requirement>
    </requirements>
  </xml>
  <xml name="stdio">
    <stdio>
      <!-- Anything other than zero is an error -->
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <!-- In case the return code has not been set propery check stderr too -->
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
    <version_command>cooler --version</version_command>
  </xml>
  <xml name="size_macro">
    <conditional name="size_source">
      <param name="size_source_selector" type="select" label="Choose the source for the chromosome sizes">
          <option value="cached">Locally cached</option>
          <option value="history">History</option>
      </param>
      <when value="cached">
          <param name="fasta_cached" type="select" label="Fasta availables">
              <options from_data_table="fasta_indexes">
                  <validator type="no_options" message="No cached fasta is available"/>
              </options>
          </param>
      </when>
      <when value="history">
        <param name="chromosomeSize" multiple="false" type="data" format="tabular" label="Select a file with the size of chromosome (One column with the chromosome names in the desired order, one column with the sizes)."/>
      </when>
    </conditional>
  </xml>
  <xml name="citation_cooler">
      <citations>
          <citation type="doi">10.1093/bioinformatics/btz540</citation>
      </citations>
  </xml>
</macros>