<?xml version="1.0"?>
<tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0">
  <description>common transformation of FASTA/Q</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk seq -q $q
-X $X
#if $n and $n != "None" and $n is not None and $n != "":
-n "$n"
#end if
-l $l
-Q $Q
-s $s
-f $f
#if $M and $M != "None" and $M is not None and $M != "":
-M "$M"
#end if
-L $L
$c
$r
$A
$C
$N
$x1
$x2
#if $in_file.ext == "fastqillumina"
 -V
#end if

$in_file
> $default]]></command>
  <inputs>
    <expand macro="in_faq"/>
    <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/>
    <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/>
    <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/>
    <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/>
    <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/>
    <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/>
    <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/>
    <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/>
    <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/>
    <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/>
    <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
    <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/>
    <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/>
    <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/>
    <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/>
    <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/>
  </inputs>
  <outputs>
    <data format_source="in_file" hidden="false" name="default"/>
  </outputs>
  <tests>
    <test>
      <!-- This is a sorry excuse for a test for a tool which does way more
           than it should, but upstream decided to put a TON of functionality
           into a single tool rather than using the single responsibility
           principle. -->
      <param name="in_file" value="seqtk_seq.fa"/>
      <param name="r" value="True"/>
      <param name="n" value=""/>
      <param name="M" value=""/>
      <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Various utilities for transforming FASTA/Q data

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