Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view alignment.xml @ 6:3c50a937d7c1 draft
Uploaded
author | bcclaywell |
---|---|
date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | 221a97bf686d |
children |
line wrap: on
line source
<tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0"> <description>with sequences in a reference package</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> <stdio> <expand macro="basic_errors"/> </stdio> <version_command>echo "$(taxit -V); $(cmalign -h | grep INFERNAL); $(esl-alimerge -h | grep Easel)"</version_command> <command interpreter="bash"> alignment-wrapper.sh ${config} </command> <inputs> <param name="refpkg" type="data" format="refpkg" label="Reference package"/> <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> </inputs> <outputs> <data name="aligned_seqs" format="fasta" label="Aligned sequences"/> <data name="aligned_scores" format="txt" label="Alignment scores"/> </outputs> <configfiles> <configfile name="config"> REFPKG="${refpkg.extra_files_path}" INPUT_SEQS="${input_seqs}" ALIGNED_SEQS="${aligned_seqs}" ALIGNED_SCORES="${aligned_scores}" </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 aligns query sequences with the reference sequences used to make the reference tree contained in the reference package and then merges the query and reference sequences. </help> <citations> <expand macro="cite_taxtastic"/> <expand macro="cite_infernal"/> </citations> </tool>