<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.1">
    <description>Converts a mascot results file to pepXML</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
    <command>mascot_to_pepxml.rb 
        $input_file 

        -o $output 

        #if $database.source_select=="built_in":
            -d $database.dbkey
        #else 
            -d $database.fasta_file
        #end if

        #if $explicit_enzyme.explicit_enzyme_use
            --enzyme $explicit_enzyme.enzyme
        #end if

        $shortid
    </command>
    <inputs>
        <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>

        <conditional name="database">
            <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
                <option value="built_in">Built-In</option>
                <option value="input_ref">Uploaded fasta file</option>
            </param>
            <when value="built_in">
                <param name="dbkey" type="select" format="text" >
                    <label>Database</label>
                    <options from_file="pepxml_databases.loc">
                        <column name="name" index="0" />
                        <column name="value" index="2" />
                    </options>
                </param>
            </when>
            <when value="input_ref">
                <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
            </when>
        </conditional>

        <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />

        <conditional name="explicit_enzyme">
            <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
            <when value="false" />
            <when value="true">
                <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
            </when>
        </conditional>

    </inputs>
    <outputs>
        <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
    </outputs>
    <tests>
        <test>
            <param name="source_select" value="input_ref"/>
              <param name="fasta_file" value="bsa.fasta"/>
                  <param name="input_file" value="F002832.dat"/>
              <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" />
        </test>
    </tests>
    <help>
        Convert mascot results from mascotdat to pepXML
    </help>
</tool>