annotate mgf_formatter.xml @ 2:51ba38ae36c2 draft default tip

planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6

<tool id="mgf_formatter" name="MGF Formatter" version="1.0.0">
    <description>convert peak lists into MGF files formatted for particular downstream applications</description>
    <requirements>
        <requirement type="package" version="1.0.0">mgf-formatter</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Unknown error, exit code non-zero" />
    </stdio>
    <command>
<![CDATA[
        mgf-formatter
            --mgf_format $mgf_format
            --output '$output'
            $itraq_filter
            #if $type.input_type == "mgf"
                $type.split_multiple_charge_states
            #end if
            $type.inputs
]]>
    </command>
    <inputs>
        <conditional name="type">
            <param name="input_type" type="select" label="Input Type">
                <option value="mzml">mzML</option>
                <option value="mzxml">mzXML</option>
                <option value="mgf">MGF</option>
            </param>
            <when value="mzml">
                <param format="mzml" name="inputs" type="data" label="Input mzML" />
            </when>
            <when value="mzxml">
                <param format="mzxml" name="inputs" type="data" label="Input mzXML" />
            </when>
            <when value="mgf">
                <param format="mgf" name="inputs" type="data" label="Input MGF" />
                <param type="boolean" name="split_multiple_charge_states" truevalue="" falsevalue="--no_split_multiple_charge_states" checked="true"
                    label="Split up scans with multiple charge states specified in MGF" />
            </when>
        </conditional>
        <param name="mgf_format" type="select" label="MGF Format">
            <option value="DEFAULT">Mascot (default, probably should use msconvert instead)</option>
            <option value="PROTEIN_PILOT">ProteinPilot</option>
            <option value="MS2PREPROC">ms2preproc</option>
            <option value="MSM">MSM</option>
        </param>
        <param name="itraq_filter" type="boolean" label="Preselect iTRAQ reporter ions"  truevalue="--itraq_filter" falsevalue=""
            help="Recent versions of ProteinPilot fail to find the correct report ions, this tool filters out extra peaks in that region to circumvent this bug if this is checked. This is an advanced option and should only be checked if you are certain you want it." />
    </inputs>
    <outputs>
        <data format="mgf" name="output" label="${mgf_format.value_label.split()[0]} formatted MGF of ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_type" value="mzml"/>
            <param name="inputs" value="Test.mzML" ftype="mzml"/>
            <param name="mgf_format" value="PROTEIN_PILOT"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="TITLE=File: Test, Sample: Sample001 (sample number 1), Elution: 0.01 min, Period: 1, Cycle(s): 47 (Experiment 1)" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
MGF Formatter convert peak lists into MGF files formatted for particular downstream applications.
]]>
    </help>
</tool>