<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>