<tool id="encyclopedia_fasta_to_prosit_csv" name="ConvertFastaToPrositCSV" version="@VERSION@.0" python_template_version="3.5">
    <description>Create Prosit CSV Input From a Protein FASTA</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        EncyclopeDIA -convert -fastatoprositcsv 
        -i '$i'
        -minCharge $minCharge
        -maxCharge $maxCharge
        -defaultCharge $defaultCharge
        -maxMissedCleavage $maxMissedCleavage
        -minMz $minMz
        -maxMz $maxMz
        -defaultNCE $defaultNCE
        #if $enzyme
            -enzyme '$enzyme'
        #end if
        -o '$output'
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="fasta" label="Protein Fasta database"/>
	<param argument="-minCharge" type="integer" value="2" min="1" max="6" label="minCharge" help="(default: 2)"/>
	<param argument="-maxCharge" type="integer" value="3" min="1" max="6" label="maxCharge" help="(default: 3)"/>
	<param argument="-defaultCharge" type="integer" value="3" min="1" max="4" label="defaultCharge" help="(default: 3)"/>
	<param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="3" label="maxMissedCleavage" help="(default: 1)"/>
	<param argument="-minMz" type="float" value="396.4" min="150.0" max="1600.0" label="minMz" help="(default: 396.4)"/>
	<param argument="-maxMz" type="float" value="1002.7" min="150.0" max="1600.0" label="maxMz" help="(default: 1002.7)"/>
	<param argument="-defaultNCE" type="integer" value="33" min="25" max="40" label="Normalized Collision Energy" help="(default: 33)"/>
        <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme" help="(default: Trypsin)">
            <option value="Trypsin">Trypsin</option>
            <option value="Lys-C">Lys-C</option>
            <option value="Lys-N">Lys-N</option>
            <option value="Arg-C">Arg-C</option>
            <option value="Glu-C">Glu-C</option>
            <option value="CNBr">CNBr</option>
            <option value="Chymotrypsin">Chymotrypsin</option>
            <option value="Pepsin A">Pepsin A</option>
            <option value="No Enzyme">No Enzyme</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="csv" label="${i.name} Prosit_input.csv"/>
    </outputs>
    <tests>
        <test>
            <param name="i" ftype="fasta" value="YeastProteinFasta5.fasta"/>
            <output name="output" ftype="csv">
                <assert_contents>
                    <has_text text="collision_energy"/>
                    <has_text text="EDFFTVFDSLLR"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Create Prosit CSV From FASTA
    ]]></help>
    <expand macro="citations" />
</tool>