Mercurial > repos > devteam > kraken2tax
comparison kraken2tax.xml @ 1:d844fdcce44e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ commit 6ae04a550dca76f641cb8ea82408fe3b068df960-dirty
| author | devteam |
|---|---|
| date | Thu, 08 Oct 2015 12:34:17 -0400 |
| parents | 065938419efe |
| children | f03c7ba8d8bc |
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| 0:065938419efe | 1:d844fdcce44e |
|---|---|
| 1 <tool id="Kraken2Tax" name="Convert Kraken" version="1.0"> | 1 <tool id="Kraken2Tax" name="Convert Kraken" version="1.1"> |
| 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">gnu_awk</requirement> |
| 5 <requirement type="package" version="8d245994d7">gb_taxonomy</requirement> | 5 <requirement type="package" version="8d245994d7">gb_taxonomy</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 ]]> |
| 11 </command> | 11 </command> |
| 12 <inputs> | 12 <inputs> |
| 13 <param format="tabular" name="input" type="data" label="Choose dataset to convert"/> | 13 <param format="tabular" name="input" type="data" label="Choose dataset to convert"/> |
| 14 <param label="Select a taxonomy database" name="ncbi_taxonomy" type="select"> | 14 <param label="Select a taxonomy database" name="ncbi_taxonomy" type="select"> |