view pplacer.xml @ 6:3c50a937d7c1 draft

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<tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0">
  <description>on a reference tree</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">
    pplacer-wrapper.sh ${config}
  </command>
  <inputs>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="query_seqs" type="data" format="fasta" label="Query alignment"/>
  </inputs>
  <outputs>
    <data name="placed_seqs" format="jplace" label="Placed sequences"/>
  </outputs>
  <configfiles>
    <configfile name="config">
REFPKG="${refpkg.extra_files_path}"
QUERY_SEQS="${query_seqs}"

PLACED_SEQS="${placed_seqs}"
    </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 places query sequences on a fixed reference phylogenetic tree
according to a reference alignment, producing taxonomic annotations which can
be used for classification and visualization.

  </help>
  <citations>
    <expand macro="cite_pplacer"/>
  </citations>
</tool>