view centrifuge_kreport.xml @ 1:ccb90fac3605 draft default tip

planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/centrifuge

<tool id="centrifuge_kreport" name="centrifuge_kreport" version="0.1.0">
  <description>Centrifuge-kreport creates Kraken-style reports from centrifuge out files</description>
  <requirements>
    <requirement type="package" version="1.0.3">centrifuge</requirement>
  </requirements>
  <command detect_errors="exit_code">
    <![CDATA[
        centrifuge-kreport
          -x '${db.fields.path}'

          #if $settings.advanced == "advanced"
            $settings.only_unique
            $settings.show_zeros
            $settings.count_table
            --min-score $settings.min_score
            --min-length $settings.min_length
          #end if

          $input > output.txt
    ]]>
  </command>
  <inputs>
    <param type="data" name="input" format="tabular"/>
    <param name="db" type="select" label="Select a reference database">
      <options from_data_table="centrifuge_indices">
        <filter type="sort_by" column="2"/>
  <validator type="no_options" message="No indexes are available for the selected input dataset"/>
</options>
    </param>
    <conditional name="settings">
      <param name="advanced" type="select" label="Specify advanced parameters">
        <option value="simple" selected="true">No, use program defaults.</option>
        <option value="advanced">Yes, see full parameter list.</option>
      </param>
      <when value="simple"></when>
      <when value="advanced">
        <param name="only_unique" type="boolean" truevalue="--only-unique" falsevalue="" checked="false" label="Only count reads that were uniquely assigned to one taxon"/>
        <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="false" label="Show clades that have zero reads, too"/>
        <param name="count_table" type="boolean" truevalue="--is-count-table" falsevalue="" label="The format of the file is 'TAXID-tab-COUNT' instead of the standard Centrifuge output format"/>
        <param name="min_score" type="integer" label="--min-score" value="0" min="0" help="Require a minimum score for reads to be counted"/>
        <param name="min_length" type="integer" label="--min-length" value="0" min="0" help="Require a minimum alignment length to the read"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="tabular" name="output" from_work_dir="output.txt" label="${tool.name} on ${on_string}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="test-data_centrifuge-kreport/defaults.tsv"/>
      <output name="output" file="defaults.tsv.kreport"/>
    </test>
  </tests>
  <help>
    <![CDATA[
centrifuge-kreport creates Kraken-style reports from centrifuge out files.
    ]]>
  </help>
  <citations>
    <citation type="doi">10.1101/gr.210641.116</citation>
  </citations>
</tool>