<?xml version="1.0"?>
<tool id="circos_gc_skew" name="GC Skew" version="@WRAPPER_VERSION@">
    <description>calculates skew over genomic sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <command detect_errors="exit_code"><![CDATA[
ln -s -f
#if $reference_genome.reference_genome_source == "history"
    '$reference_genome.history_item'
#else
    '$reference_genome.builtin.fields.path'
#end if
reference.fa &&

python '$__tool_directory__/gc_skew.py' reference.fa '$window' '$output'
    ]]></command>
    <inputs>
      <conditional name="reference_genome">
        <param label="Source for reference genome" name="reference_genome_source" type="select">
          <option selected="True" value="history">Use a genome from history</option>
          <option value="builtin">Use a built-in genome"</option>
        </param>
        <when value="history">
          <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
        </when>
        <when value="builtin">
          <param label="Select a reference genome" name="builtin" type="select">
            <options from_data_table="all_fasta">
              <filter column="2" type="sort_by" />
              <validator message="No genomes are available for the selected input dataset" type="no_options" />
            </options>
          </param>
        </when>
      </conditional>
      <param argument="window" type="integer" min="1" value="100000" label="Window size" />
    </inputs>
    <outputs>
      <data name="output" format="bigwig" />
    </outputs>
    <tests>
        <test>
            <conditional name="reference_genome">
                <param name="reference_genome_source" value="history" />
                <param name="history_item" value="gc_skew/1.fa" ftype="fasta"/>
            </conditional>
            <param name="window" value="2" />
            <output name="output" file="gc_skew/1.bw" ftype="bigwig" />
        </test>
    </tests>
    <help><![CDATA[
Calculate GC skew (G-C)/(G+C) for multiple windows along the sequence.

Returns a list of ratios (floats), controlled by the length of the sequence and the size of the window.

Returns 0 for windows without any G/C by handling zero division errors.

Does NOT look at any ambiguous nucleotides.
    ]]></help>
    <expand macro="citations" />
</tool>