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"planemo upload for repository https://github.com/phac-nml/promer commit 09ae227a84e31c9c56f58815b1a0c8c0e0a7900e"
author nml
date Tue, 17 Dec 2019 15:55:27 -0500
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<tool id="promer4_substitutions" name="report substitutions" version="1.2">
    <description>aligns two sets of contigs and reports amino acid substitutions between them</description>
    <requirements>
          <requirement type="package" version="3.5.6">python</requirement>
          <requirement type="package" version="4.0.0beta2">mummer4</requirement>
          <requirement type="package" version="1.68">biopython</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        python '$__tool_directory__/promer_substitutions.py' '$reference_fasta' '$query_fasta'

    ]]></command>

    <inputs>
        <param name="reference_fasta" type="data" format="fasta" optional="false" label="Reference FASTA"/>
        <param name="query_fasta" type="data" format="fasta" optional="false" label="Query FASTA" />
    </inputs>

    <outputs>
        <data format="tabular" label="substitutions" name="output_substitutions" from_work_dir="snps.tab" />
        <data format="fasta" label="contigs" name="output_contigs" from_work_dir="contigs.fasta" />
    </outputs>

    <tests>
        <test>
            <param name="query_fasta" value="query.fasta" />
            <param name="reference_fasta" value="reference.fasta" />
            <output name="output_substitutions" file="snps.tab" ftype="tabular" />
            <output name="output_contigs" file="contigs.fasta" ftype="fasta" />
        </test>
    </tests>

    <help><![CDATA[
Report Substitutions
=====================

Aligns a set of query contigs against a set of reference contigs and reports the amino acid differences between the two sets of contigs using MUMmer4 (promer):

Kurtz, Stefan et al. “Versatile and Open Software for Comparing Large Genomes.” Genome Biology 5.2 (2004): R12. PMC. Web. 22 Aug. 2018.

The alignments are performed in amino acid space. Only the substitutions from the best set of global alignments are reported in the output.

------
Inputs
------

1. Query FASTA: A nucleotide or amino acid FASTA query file.
2. Reference FASTA: A nucleotide or amino acid FASTA reference file.

-------
Outputs
-------

1. substitions: A tabular file detailing subsitutions between aligned contigs.

]]></help>
    <citations>
    </citations>
</tool>