<tool id="clinker" name="clinker" version="@VERSION@+galaxy0">
    <description> Automatic creation of publication-ready gene cluster comparison figures</description>
    <macros>
        <token name="@VERSION@">0.0.23</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">clinker-py</requirement>
    </requirements>
    <version_command>clinker --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        mkdir gbk &&
        #for $counter, $input in enumerate($gbk):
            #set $_input_file = re.sub(r'(\s|\(|\)|:|!)|\.gbk', '_', str($input.element_identifier))
            ln -sf '$input' 'gbk/${$_input_file}.gbk' &&
        #end for
        clinker
        $no_align
        --identity $identity
        --jobs \${GALAXY_SLOTS:-4}
        -dl ","
        -dc 4
        #if $output
            --output am.csv
        #end if
        gbk/*.gbk
        -p plot.html
    ]]>    </command>

    <inputs>
        <param name="gbk" type="data" format="genbank" multiple="true" label="Genbank files"/>
        <param argument="no_align" type="boolean" truevalue="--no_align" falsevalue="" checked="false" label="Do not align clusters" />
        <param argument="identity" type="float" min="0.1" value="0.3" max="1.0" label="Minimum alignment sequence identity" />
        <param argument="output" type="boolean" truevalue="--output" falsevalue="" checked="false" label="Save alignments to file" />
    </inputs>
    <outputs>
        <data name="alignment" format="txt" from_work_dir="am.csv" label="${tool.name} on ${on_string} Alignment file">
            <filter>output is True</filter>
        </data>
        <data name="plot" format="html" from_work_dir="plot.html" label="${tool.name} on ${on_string} Plot" />
    </outputs>
    <help><![CDATA[
        Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using clustermap.js) that can be extensively tweaked before being exported as an SVG file.

        See https://github.com/gamcil/clinker
    ]]>    </help>
</tool>