<tool id="PHYLO_preclassification" name="Generate database" version="1.2.0">
  <description>for classification</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">
    preclassification-wrapper.sh ${config}
  </command>
  <inputs>
    <param name="dedup_info" type="data" format="csv" label="Deduplication info"/>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/>
    <param name="placed_seqs" type="data" format="jplace" label="Placements"/>
  </inputs>
  <outputs>
    <data name="reduped_seqs" format="jplace" label="Reduped placements"/>
    <data name="class_db" format="sqlite3" label="Placement database"/>
  </outputs>
  <configfiles>
    <configfile name="config">
DEDUP_INFO="${dedup_info}"
REFPKG="${refpkg.extra_files_path}"
NBC_SEQS="${nbc_seqs}"
PLACED_SEQS="${placed_seqs}"

REDUPED_SEQS="${reduped_seqs}"
CLASS_DB="${class_db}"
    </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 outputs the classifications made by ``pplacer`` to a database for use
in taxonomic classification.

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