view seqtk_mergefa.xml @ 1:61718851f199 draft

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<?xml version="1.0"?>
<tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
  <description>merge two FASTA/Q files</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk mergefa -q $q
$i
$m
$r
$h

$in_fa1
$in_fa2

> $default]]></command>
  <inputs>
    <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
    <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
    <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/>
    <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/>
    <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
    <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
    <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/>
  </inputs>
  <outputs>
    <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/>
  </outputs>
  <tests>
    <test>
      <param name="in_fa1" value="seqtk_mergefa1.fa"/>
      <param name="in_fa2" value="seqtk_mergefa2.fa"/>
      <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
    </test>
    <test>
      <param name="in_fa1" value="seqtk_mergefa1.fa"/>
      <param name="in_fa2" value="seqtk_mergefa2.fa"/>
      <param name="m" value="True" />
      <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Merges two fasta files, using ambiguity codes

::

    # seq1.fa
    >test0
    ACTGACTGAAA

    # seq2.fa
    >test0
    ACTGAMTGCGN

In the following the `-m` option has been set to highlight seqtk-mergefa's features.

::

    >test0
    ACTGACTGxxa

@ATTRIBUTION@
]]></help>
</tool>