comparison kraken2tax.xml @ 2:f03c7ba8d8bc draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ commit a69aac7457497eae5d4ee8b1f2617b4039851ebc

1:d844fdcce44e

<tool id="Kraken2Tax" name="Convert Kraken" version="1.1">
  <description>data to Galaxy taxonomy representation</description>
    <requirements>
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
        <requirement type="package" version="8d245994d7">gb_taxonomy</requirement>
    </requirements>
  <command>
<![CDATA[
  awk '{ print \$${read_name}, \$${tax_id} }' OFS="\t" "${input}" | taxonomy-reader "${ncbi_taxonomy.fields.path}/names.dmp" "${ncbi_taxonomy.fields.path}/nodes.dmp" 1 > "${out_file}"
]]>

  </help>
  <citations>
    <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    <citation type="doi"> 10.1101/gr.094508.109</citation>
  </citations>
</tool>

2:f03c7ba8d8bc

<tool id="Kraken2Tax" name="Convert Kraken" version="1.2">
  <description>data to Galaxy taxonomy representation</description>
    <requirements>
        <requirement type="package" version="4.1.0">gawk</requirement>
        <requirement type="package" version="1.0.0">gb_taxonomy_tools</requirement>
    </requirements>
  <command>
<![CDATA[
  awk '{ print \$${read_name}, \$${tax_id} }' OFS="\t" "${input}" | taxonomy-reader "${ncbi_taxonomy.fields.path}/names.dmp" "${ncbi_taxonomy.fields.path}/nodes.dmp" 1 > "${out_file}"
]]>

  </help>
  <citations>
    <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    <citation type="doi">10.1101/gr.094508.109</citation>
  </citations>
</tool>