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comparison kraken2tax.xml @ 3:e834f2b46f3a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ commit 45d0409859aca5b099dba7e0acd472f5703240e1
author devteam
date Fri, 29 Sep 2023 14:38:19 +0000
parents acb48a12c0f2
children
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2:acb48a12c0f2 3:e834f2b46f3a
1 <tool id="Kraken2Tax" name="Convert Kraken" version="1.2"> 1 <tool id="Kraken2Tax" name="Convert Kraken" version="1.2+galaxy0">
2 <description>data to Galaxy taxonomy representation</description> 2 <description>data to Galaxy taxonomy representation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.1.0">gawk</requirement> 4 <requirement type="package" version="5.1.0">gawk</requirement>
5 <requirement type="package" version="1.0.0">gb_taxonomy_tools</requirement> 5 <requirement type="package" version="1.0.1">gb_taxonomy_tools</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 <![CDATA[ 8 <![CDATA[
9 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}" 9 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}"
10 ]]> 10 ]]>