<tool id="smart_domains" name="SMART domains" version="0.1.0">
    <description>Search domains in protein sequences using SMART</description>
    <requirements>
        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
        <requirement type="package" version="2.90">perl-json</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
perl '$__tool_directory__/smart-domain.pl'
--inputFile='$inputFile'
$Pfam
$SignalP
$Repeats
$DISEMBL
$Schnipsel
$outputFormat
    ]]></command>
    <inputs>
        <param name="inputFile" type="data" format="fasta" label="Protein sequences" help="In FASTA format" />
        <param name="Pfam" type="boolean" truevalue="--includePfam" falsevalue="" label="Include Pfam domains" argument="--includePfam" />
        <param name="SignalP" type="boolean" truevalue="--includeSignalP" falsevalue="" label="Include signal peptide predictions" argument="--includeSignalP" />
        <param name="Repeats" type="boolean" truevalue="--includeRepeats" falsevalue="" label="Include internal repeat predictions" argument="--includeRepeats" />
        <param name="DISEMBL" type="boolean" truevalue="--includeDISEMBL" falsevalue="" label="Include predictions of internal protein disorder" argument="--includeDISEMBL" />
        <param name="Schnipsel" type="boolean" truevalue="--includeSchnipsel" falsevalue="" label="Include predictions of outlier homologues and homologues of known structures" argument="--includeSchnipsel" />
        <param name="outputFormat" type="select" label="Output format">
            <option value="--outputFormat=txt" selected="true">Text</option>
            <option value="--outputFormat=tabular">Tabular</option>
            <option value="--outputFormat=json">JSON</option>
        </param>
    </inputs>
    <outputs>
        <collection name="output_lists" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+)_SMART_results\.(?P&lt;ext&gt;.+)" directory="SMART_results" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" ftype="fasta" value="seq.fa" />
            <param name="Pfam" value="true" />
            <param name="SignalP" value="false" />
            <param name="Repeats" value="false" />
            <param name="DISEMBL" value="false" />
            <param name="Schnipsel" value="false" />
            <param name="outputFormat" value="--outputFormat=txt" />
            <output_collection name="output_lists" type="list" count="12">
                <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.txt" ftype="txt" />
                <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.txt" ftype="txt" />
                <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.txt" ftype="txt" />
                <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.txt" ftype="txt" />
                <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.txt" ftype="txt" />
                <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.txt" ftype="txt" />
                <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.txt" ftype="txt" />
                <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.txt" ftype="txt" />
                <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.txt" ftype="txt" />
                <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.txt" ftype="txt" />
                <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.txt" ftype="txt" />
                <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.txt" ftype="txt" />
            </output_collection>
        </test>
        <test>
            <param name="inputFile" ftype="fasta" value="seq.fa" />
            <param name="Pfam" value="true" />
            <param name="SignalP" value="false" />
            <param name="Repeats" value="false" />
            <param name="DISEMBL" value="false" />
            <param name="Schnipsel" value="false" />
            <param name="outputFormat" value="--outputFormat=json" />
            <output_collection name="output_lists" type="list" count="12">
                <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.json" ftype="json" compare="sim_size" />
                <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.json" ftype="json" compare="sim_size" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
A simple tool to search domains in multiple protein sequences contained in a FASTA file using the `SMART`_ web service.

Written by Ivica Letunic <ivica@letunic.com>

Modified by Anil Thanki <Anil.Thanki@earlham.ac.uk> to parse output in JSON and tabular format to adapt in Galaxy

.. _SMART: http://smart.embl.de/
    ]]></help>
    <citations>
        <citation type="doi">10.1073/pnas.95.11.5857</citation>
        <citation type="doi">10.1093/nar/gku949</citation>
    </citations>
</tool>