Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view preprocessing.xml @ 6:3c50a937d7c1 draft
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author | bcclaywell |
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date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | 221a97bf686d |
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<tool id="PHYLO_preprocessing" name="Deduplicate sequences" version="3.0.0"> <description>in preparation for alignment and placement</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> <stdio> <expand macro="basic_errors"/> </stdio> <version_command>echo "pplacer $(pplacer --version)"</version_command> <command interpreter="bash"> preprocessing-wrapper.sh ${config} </command> <inputs> <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/> </inputs> <outputs> <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/> <data name="dedup_info" format="csv" label="Deduplication info"/> </outputs> <configfiles> <configfile name="config"> INPUT_SEQS="${input_seqs}" SPLIT_MAP="${split_map}" DEDUP_SEQS="${dedup_seqs}" DEDUP_INFO="${dedup_info}" </configfile> </configfiles> <!-- The contents of the help tag is parsed as reStructuredText. Please see help-template.rst for examples of commonly-used sections in other Galaxy tools. --> <help> .. class:: infomark **What it does** This tool deduplicates input sequences in preparation for alignment and placement. </help> <citations> <expand macro="cite_pplacer"/> </citations> </tool>