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comparison kraken2tax.xml @ 2:f03c7ba8d8bc draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ commit a69aac7457497eae5d4ee8b1f2617b4039851ebc
author devteam
date Wed, 26 Apr 2017 14:11:06 -0400
parents d844fdcce44e
children 50bd98b3ae5a
comparison
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1:d844fdcce44e 2:f03c7ba8d8bc
1 <tool id="Kraken2Tax" name="Convert Kraken" version="1.1"> 1 <tool id="Kraken2Tax" name="Convert Kraken" version="1.2">
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">gnu_awk</requirement> 4 <requirement type="package" version="4.1.0">gawk</requirement>
5 <requirement type="package" version="8d245994d7">gb_taxonomy</requirement> 5 <requirement type="package" version="1.0.0">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 ]]>
94 94
95 95
96 </help> 96 </help>
97 <citations> 97 <citations>
98 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> 98 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
99 <citation type="doi"> 10.1101/gr.094508.109</citation> 99 <citation type="doi">10.1101/gr.094508.109</citation>
100 </citations> 100 </citations>
101 </tool> 101 </tool>
102 102
103 103