annotate fastg2protlib-validate.xml @ 0:6b226c5907a1 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"

<tool id="fastg2protlib-validate" name="FASTG2Protlib-Validate" version="@VERSION@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="pkg_requirement" />
    <description>Validate a candidate protein library</description>

    <command detect_errors="exit_code">
        <![CDATA[
        python '$__tool_directory__/app_validate.py' 
        -d '$database_file'
        -f $fdr_level
        -x '$decoy_header'
        '$tabular_file'
        ]]>
    </command>
    <inputs>
        <param name="tabular_file" type="data" format="txt" label="MSGF+ tabular file" />
        <param name="database_file" type="data" format="sqlite" label="Database Name"/>
        <param name="fdr_level" type="float" value="0.10" label="FDR value for validation."/>
        <param name="decoy_header" type="text" value="XXX_" label="Decoy protein header"/>
    </inputs>
    <outputs>
        <data name="protein_fasta" format="fasta" from_work_dir="protein.fasta" label="Validated protein library"/>
        <data name="protein_score" format="csv" from_work_dir="protein_scores.csv" label="Protein scores"/>
    </outputs>
    <tests>
        <test>
            <param name="tabular_file" value="mgf_tst.tab" />
            <param name="database_file" value="tst_valid.db" />
            <param name="fdr_level" value="0.10" />
            <param name="decoy_header" value="XXX_" />
            <output name="protein_fasta">
                <assert_contents>
                    <has_text text="RYSRPLSHL" />
                </assert_contents>
            </output>
        </test>
    </tests>    
    <expand macro="help-text" />
</tool>