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<tool id="draw_circos" name="PIMA: draw circos" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>plot of assembly v. reference alignment</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_conffiles.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0797</edam_topic>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0337</edam_operation>
    </edam_operations>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
mkdir -p circos_dir &&
mkdir -p output_png_dir &&

cp '$circos_conf' 'circos_dir/circos.conf' &&
cp '$ideogram_conf' 'circos_dir/ideogram.conf' &&
cp '$tick_base_conf' 'circos_dir/tick_base.conf' &&

#if $reference_source.reference_source_selector == 'history':
    ln -f -s '$reference_source.ref_file' reference.fa &&
#else:
    ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
#end if

python '$__tool_directory__/draw_circos.py'
--circos_conf 'circos_dir/circos.conf'
--dnadiff_1coords_file '$dnadiff_1coords_file'
--output_png_dir 'output_png_dir'
--reference_file 'reference.fa'
--reference_sequence_lengths_file '$reference_sequence_lengths_file'
--tick_base_conf 'circos_dir/tick_base.conf'
    ]]></command>
    <configfiles>
        <expand macro="configfile_circos_conf"/>
        <expand macro="configfile_ideogram_conf"/>
        <expand macro="configfile_tick_base_conf"/>
    </configfiles>
    <inputs>
        <param argument="dnadiff_1coords_file" type="data" format="tabular,tsv" label="DNAdiff 1coords tabular file"/>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?">
                <option value="cached">Use a cached genome index</option>
                <option value="history">Select a genome from the history and build the index</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select reference genome">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No reference genomes are available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta,fastq" label="Select the reference sequence" help="You can upload a FASTA file and use it as reference"/>
            </when>
        </conditional>
        <param name="reference_sequence_lengths_file" type="data" format="tabular" label="Reference sequences lengths tabular file"/>
    </inputs>
    <outputs>
        <collection name="circos_png" type="list" format="png">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png)" directory="output_png_dir"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="dnadiff_1coords_file" value="dnadiff_1coords.tabular" ftype="tabular"/>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="ref_genome.fasta"/>
            </conditional>
            <param name="reference_sequence_lengths_file" value="ref_sequence_lengths.tabular" ftype="tabular"/>
            <output_collection name="circos_png" type="list" count="3">
                <element name="chromosome" ftype="png">
                    <assert_contents>
                        <has_size value="121172" delta="1000"/>
                    </assert_contents>
                </element>
                <element name="pXO1" ftype="png">
                    <assert_contents>
                        <has_size value="179913" delta="1000"/>
                    </assert_contents>
                </element>
                <element name="pXO2" ftype="png">
                    <assert_contents>
                        <has_size value="169070" delta="1000"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="dnadiff_1coords_file" value="dnadiff_1coords.tabular" ftype="tabular"/>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="ref_genome"/>
            </conditional>
            <param name="reference_sequence_lengths_file" value="ref_sequence_lengths.tabular" ftype="tabular"/>
            <output_collection name="circos_png" type="list" count="3">
                <element name="chromosome" ftype="png">
                    <assert_contents>
                        <has_size value="121172" delta="1000"/>
                    </assert_contents>
                </element>
                <element name="pXO1" ftype="png">
                    <assert_contents>
                        <has_size value="179913" delta="1000"/>
                    </assert_contents>
                </element>
                <element name="pXO2" ftype="png">
                    <assert_contents>
                        <has_size value="169070" delta="1000"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Renders circos plots of the PIMA assembly versus the reference alignemnt.
    ]]></help>
    <expand macro="citations"/>
</tool>