<tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2">
    <description>Definition of experimental design used for record keeping and writing spectra data.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <command detect_errors="exit_code"><![CDATA[
        sh ${ramclustr_define_experiment_cli}
    ]]>
    </command>
    <configfiles>
        <configfile name="ramclustr_define_experiment_cli">
            python3 ${__tool_directory__}/ramclustr_define_experiment_wrapper.py \
            --Experiment "$design.Experiment" \
            --Species "$design.Species" \
            --Sample "$design.Sample" \
            --Contributer "$design.Contributor" \
            --platform "$platform.platform_choice.choice" \
            #if $platform.platform_choice.choice == "GC-MS":
                --chrominst "$platform.platform_choice.chrominst" \
                --msinst "$platform.platform_choice.msinst" \
                --column "$platform.platform_choice.column" \
                --InletTemp "$platform.platform_choice.InletTemp" \
                --TransferTemp "$platform.platform_choice.TransferTemp" \
                --mstype "$platform.platform_choice.gc_mstype" \
                --msmode "$platform.platform_choice.msmode" \
                --ionization "$platform.platform_choice.gc_ionization" \
                --msscanrange "$platform.platform_choice.msscanrange" \
                --scantime "$platform.platform_choice.scantime" \
                --deriv "$platform.platform_choice.deriv" \
                --MSlevs "$platform.platform_choice.MSlevs" \
            #else:
                --chrominst "$platform.platform_choice.chrominst" \
                --msinst "$platform.platform_choice.msinst" \
                --column "$platform.platform_choice.column" \
                --solvA "$platform.platform_choice.solvA" \
                --solvB "$platform.platform_choice.solvB" \
                --CE1 "$platform.platform_choice.CE1" \
                --CE2 "$platform.platform_choice.CE2" \
                --mstype "$platform.platform_choice.lc_mstype" \
                --msmode "$platform.platform_choice.msmode" \
                --ionization "$platform.platform_choice.lc_ionization" \
                --colgas "$platform.platform_choice.colgas" \
                --msscanrange "$platform.platform_choice.msscanrange" \
                --conevol "$platform.platform_choice.conevol" \
                --MSlevs "$platform.platform_choice.MSlevs" \
            #end if
            --output_file "$RAMClustR_experiment"
        </configfile>
    </configfiles>
    <inputs>
        <section name="design" title="Experimental Design" expanded="true">
            <param name="Experiment" type="text" label="Experiment name (no spaces).">
                <validator type="empty_field"/>
            </param>
            <param name="Species" type="text" label="Genus species from which samples are derived."/>
            <param name="Sample" type="text" label="Type of sample (e.g., serum, leaf)."/>
            <param name="Contributor" type="text" label="Your or your PI's name."/>
        </section>

        <section name="platform" title="Platform" expanded="true">
            <conditional name="platform_choice">
                <param name="choice" type="select" label="Choose platform:">
                    <option value="GC-MS" selected="true">GC-MS</option>
                    <option value="LC-MS">LC-MS</option>
                </param>
                <when value="GC-MS">
                    <param name="chrominst" type="text" label="Model of GC instrument."/>
                    <param name="msinst" type="text" label="Model of MS instrument."/>
                    <param name="column" type="text" label="Column description."/>
                    <param name="InletTemp" type="text" label="Temperature of inlet."/>
                    <param name="TransferTemp" type="text" label="Temperature of GC to MS transfer line."/>
                    <param name="gc_mstype" type="select" label="Type of mass spectrometer:">
                        <option value="QQQ" selected="true">QQQ</option>
                        <option value="TOF">TOF</option>
                        <option value="QTOF">QTOF</option>
                        <option value="Orbi">Orbi</option>
                        <option value="Q">Q</option>
                    </param>
                    <param name="msmode" type="select" label="Ion mode:">
                        <option value="positive" selected="true">positive</option>
                        <option value="negative">negative</option>
                    </param>
                    <param name="gc_ionization" type="select" label="Ionization:">
                        <option value="EI" selected="true">EI</option>
                        <option value="AP">AP</option>
                        <option value="CI">CI</option>
                    </param>
                    <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
                    <param name="scantime" type="float" value="0.2" label="Time for each full scan spectrum (e.g. 0.2 seconds)."/>
                    <param name="deriv" type="select" label="Derivitization:">
                        <option value="TMS" selected="true">TMS</option>
                        <option value="TBDMS">TBDMS</option>
                        <option value="None">None</option>
                    </param>
                    <param name="MSlevs" type="float"  value="1" label="Number of levels of energy acquired - 1 typically."/>
                </when>
                <when value="LC-MS">
                    <param name="chrominst" type="text" label="Model of LC instrument."/>
                    <param name="msinst" type="text" label="Model of MS instrument."/>
                    <param name="column" type="text" label="Column description."/>
                    <param name="solvA" type="text" label="Solvent A composition."/>
                    <param name="solvB" type="text" label="Solvent B composition."/>
                    <param name="CE1" type="text" label="Collision energy of acquisition of MS data."/>
                    <param name="CE2" type="text" label="Collision energy of acquisition for MSe/idMSMS data (when applicable)."/>
                    <param name="lc_mstype" type="select" label="Type of mass spectrometer:">
                        <option value="QQQ" selected="true">QQQ</option>
                        <option value="TOF">TOF</option>
                        <option value="QTOF">QTOF</option>
                        <option value="Orbi">Orbi</option>
                        <option value="Q">Q</option>
                    </param>
                    <param name="msmode" type="select" label="Ion mode:">
                        <option value="positive" selected="true">positive</option>
                        <option value="negative">negative</option>
                    </param>
                    <param name="lc_ionization" type="select" label="Ionization:">
                        <option value="ESI" selected="true">ESI</option>
                        <option value="APCI">APCI</option>
                    </param>
                    <param name="colgas" type="text" label="Gas used for collisional dissociation."/>
                    <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
                    <param name="conevol" type="text" label="Cone voltage used for acquisition."/>
                    <param name="MSlevs" type="float" value="1" label="number of levels of energy in XCMS object data - 1 typically."/>
                </when>
            </conditional>
        </section>
    </inputs>

    <outputs>
        <data label="RAMClustR experiment definition" name="RAMClustR_experiment" format="csv" />
    </outputs>

    <tests>
        <test><!-- TEST 1 -->
            <section name="design">
                <param name="Experiment" value="experiment_gc"/>
                <param name="Species" value="mus musculus"/>
                <param name="Sample" value="serum"/>
                <param name="Contributor" value="recetox"/>
            </section>
            <section name="platform">
                <section name="platform_choice">
                    <param name="choice" value="GC-MS"/>
                    <param name="chrominst" value="ISQ 7000"/>
                    <param name="msinst" value="ISQ7K-VPI"/>
                    <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
                    <param name="InletTemp" value="33"/>
                    <param name="TransferTemp" value="23"/>
                    <param name="gc_mstype" value="QTOF"/>
                    <param name="msmode" value="positive"/>
                    <param name="gc_ionization" value="AP"/>
                    <param name="msscanrange" value="100"/>
                    <param name="scantime" value="0.2"/>
                    <param name="deriv" value="TMS"/>
                    <param name="MSlevs" value="1.0"/>
                </section>
            </section>
            <output name="RAMClustR_experiment" file="gc-ramclustr-define-experiment.csv" ftype="csv"/>
        </test>
        <test><!-- TEST 2 -->
            <section name="design">
                <param name="Experiment" value="experiment_lc"/>
                <param name="Species" value="mus musculus"/>
                <param name="Sample" value="serum"/>
                <param name="Contributor" value="recetox"/>
            </section>
            <section name="platform">
                <section name="platform_choice">
                    <param name="choice" value="LC-MS"/>
                    <param name="chrominst" value="UltiMateX 3000 BioRS System"/>
                    <param name="msinst" value="FSN04-10000"/>
                    <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
                    <param name="solvA" value="H20"/>
                    <param name="solvB" value="CO2"/>
                    <param name="CE1" value="50"/>
                    <param name="CE2" value="100"/>
                    <param name="lc_mstype" value="Q"/>
                    <param name="msmode" value="negative"/>
                    <param name="lc_ionization" value="ESI"/>
                    <param name="colgas" value="He"/>
                    <param name="msscanrange" value="1000"/>
                    <param name="conevol" value="12"/>
                    <param name="MSlevs" value="1.0"/>
                </section>
            </section>
            <output name="RAMClustR_experiment" file="lc-ramclustr-define-experiment.csv" ftype="csv"/>
        </test>
    </tests>

    <help>
        <![CDATA[
            @HELP_experiment@
        ]]>
    </help>

    <expand macro="citations" />
</tool>