<?xml version="1.0"?>
<tool id="seqtk_mutfa" name="seqtk_mutfa" version="@TOOL_VERSION@.1">
    <description>point mutate FASTA at specified positions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk mutfa
'$in_file'
'$in_snp'
@CONDITIONAL_GZIP_OUT@
    ]]></command>
    <inputs>
        <expand macro="in_faq"/>
        <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" label="Mutated $in_file.name"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_mutfa.fa"/>
            <param name="in_snp" value="seqtk_mutfa.snp"/>
            <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_mutfa.fa.gz" ftype="fasta.gz"/>
            <param name="in_snp" value="seqtk_mutfa.snp"/>
            <output name="default" file="seqtk_mutfa.out.gz" ftype="fasta.gz"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.

::

    # Input fasta
    >test0
    ACTGACTGAA

    # Input SNP file
    test0 1 . G
    test0 4 . A

This will effect the desired mutations in the output file

::

    # Output result
    >test0
    GCTAACTGAA

@ATTRIBUTION@
    ]]></help>
    <expand macro="citation" />
</tool>