Mercurial > repos > bcclaywell > microbiome_pplacer_suite
comparison preclassification.xml @ 6:3c50a937d7c1 draft
Uploaded
| author | bcclaywell |
|---|---|
| date | Wed, 15 Apr 2015 19:14:23 -0400 |
| parents | d4690e65afcd |
| children |
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| 5:2d023c621bd0 | 6:3c50a937d7c1 |
|---|---|
| 1 <tool id="PHYLO_preclassification" name="Generate database" version="1.2.0"> | 1 <tool id="PHYLO_preclassification" name="Generate database" version="1.2.0"> |
| 2 <description>for classification</description> | 2 <description>for classification</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 3 <requirements> | 6 <requirements> |
| 4 <requirement type="package">yapp_env</requirement> | 7 <requirement type="package">yapp_env</requirement> |
| 5 </requirements> | 8 </requirements> |
| 6 <macros> | 9 <stdio> |
| 7 <import>macros.xml</import> | 10 <expand macro="basic_errors"/> |
| 8 </macros> | 11 </stdio> |
| 9 <version_command>echo "guppy $(guppy --version)"</version_command> | 12 <version_command>echo "pplacer $(pplacer --version)"</version_command> |
| 10 <command interpreter="bash"> | 13 <command interpreter="bash"> |
| 11 preclassification-wrapper.sh ${config} | 14 preclassification-wrapper.sh ${config} |
| 12 </command> | 15 </command> |
| 13 <stdio> | |
| 14 <expand macro="basic_errors"/> | |
| 15 </stdio> | |
| 16 <inputs> | 16 <inputs> |
| 17 <param name="dedup_info" type="data" format="csv" label="Deduplication info"/> | 17 <param name="dedup_info" type="data" format="csv" label="Deduplication info"/> |
| 18 <param name="refpkg" type="data" format="refpkg" label="Reference package"/> | 18 <param name="refpkg" type="data" format="refpkg" label="Reference package"/> |
| 19 <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/> | 19 <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/> |
| 20 <param name="placed_seqs" type="data" format="jplace" label="Placements"/> | 20 <param name="placed_seqs" type="data" format="jplace" label="Placements"/> |
| 45 | 45 |
| 46 This tool outputs the classifications made by ``pplacer`` to a database for use | 46 This tool outputs the classifications made by ``pplacer`` to a database for use |
| 47 in taxonomic classification. | 47 in taxonomic classification. |
| 48 | 48 |
| 49 </help> | 49 </help> |
| 50 <citations> | |
| 51 <expand macro="cite_pplacer"/> | |
| 52 </citations> | |
| 50 </tool> | 53 </tool> |