comparison preprocessing.xml @ 0:d4690e65afcd draft

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0:d4690e65afcd

<tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0">
  <description>in preparation for phylogenetic placement</description>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <macros>
    <import>macros.xml</import>
  </macros>
  <version_command>echo "guppy $(guppy --version)"</version_command>
  <command interpreter="bash">
    preprocessing-wrapper.sh ${config}
  </command>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <inputs>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
    <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
  </inputs>
  <outputs>
    <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/>
    <data name="dedup_info" format="csv" label="Deduplication info"/>
    <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
    <data name="aligned_scores" format="txt" label="Alignment scores"/>
  </outputs>
  <configfiles>
    <configfile name="config">
REFPKG="${refpkg.extra_files_path}"
INPUT_SEQS="${input_seqs}"
SPLIT_MAP="${split_map}"

DEDUP_SEQS="${dedup_seqs}"
DEDUP_INFO="${dedup_info}"
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>
</tool>