<?xml version="1.0"?>
<tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
  <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
> $default]]></command>
  <inputs>
    <expand macro="in_faq"/>
    <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
  </inputs>
  <outputs>
    <data format_source="in_file" hidden="false" name="default" 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>
  </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>
</tool>