annotate psm_validation.xml @ 1:b71c651e7950 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c"

    <tool id="psmvalidator" name="PSM-Fragment Validator" version="@VERSION@+galaxy@VERSION_SUFFIX@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <description>Validate PSMs against Ion Fragmentation</description>
    <expand macro="pkg_requirement" />
    <command detect_errors="exit_code">
        <![CDATA[
        python '$__tool_directory__/application.py' 
            -d '$mz_db_name'
            -p '$peptide_sequences'
            #if $neutral_loss_ions:
                -n
            #end if
            #if $internal_ions:
                -i
            #end if
            -b $b_ion_run
            -y $y_ion_run
            -e $epsilon
            #if $b_ion_run < 0:
                --test
            #end if
        ]]>
    </command>
    <inputs>
        <param name="mz_db_name" type="data" format="mz.sqlite" label="MZSQLite DB" />
        <param name="peptide_sequences" type="data" format="tabular" label="Peptide Sequence List" />
        <param name="b_ion_run" type="integer" value="2" label="Consecutive B-Ions" />
        <param name="y_ion_run" type="integer" value="2" label="Consecutive Y-Ions" />
        <param name="neutral_loss_ions" type="boolean" checked="True" label="Use Neutral Loss" />
        <param name="internal_ions" type="boolean" checked="True" label="Use Internals" />
        <param name="epsilon" type="float" value="0.5" label="Fragment Tolerance" />
    </inputs>
    <outputs>
        <data name="html_output" format="html" from_work_dir="index.html" label="PSM Ion Fragementation Report" />
        <data name="text_output" format="tabular" from_work_dir="results.tab" label="Tabular Results" />
    </outputs>
    <tests>
        <test>
            <param name="mz_db_name" value="test.db" />
            <param name="peptide_sequences" value="test-peptides.txt" />
            <param name="b_ion_run" value="-99" />
            <param name="y_ion_run" value="-99" />
            <param name="neutral_loss_ions" value="True" />
            <param name="internal_ions" value="True" />
            <param name="epsilon" value="0.5" />
            <output name="html_output">
                <assert_contents>
                    <has_text text="success" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <expand macro="help-text" />
</tool>