view maxquant_phosphopeptide_intensity.xml @ 0:b09ed1684301 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant_phosphopeptide_intensity commit c41945617c468ca66813c95de6a5e6fe0edb0c15"

<tool id="maxquant_phosphopeptide_intensity" name="MaxQuant Phosphopeptide Intensity" version="0.1.0" python_template_version="3.5">
    <description>for each sample</description>
    <requirements>
        <requirement type="package" version="1.14.2">r-data.table</requirement>
        <requirement type="package" version="1.7.1">r-optparse</requirement>
        <requirement type="package" version="1.4.0">r-stringr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/MaxQuantProcessingScript.R' 
-i '$phospho_sites' 
--enriched $enriched
--phosphoCol $phosphoCol
--numSamples $numSamples
--startCol $startCol 
--intervalCol $intervalCol
--localProbCutoff $localProbCutoff
--collapse_func $collapse_func
-o phosphopeptide_intensities.tsv
&& head phosphopeptide_intensities.tsv

    ]]></command>
    <inputs>
        <param name="phospho_sites" type="data" format="tabular" label="MaxQuant Phospho (STY)Sites.txt"/>
        <param name="phosphoCol" type="data_column" numerical="false" data_ref="phospho_sites" label="Column: Number of Phospho (STY)" />
        <param name="numSamples" type="integer" value="1" min="1" label="Number of samples or runs"/>
        <param name="startCol" type="data_column" numerical="false" data_ref="phospho_sites" label="Column: Intensity of the first sample" />
        <param name="intervalCol" type="integer" value="1" min="1" label="Interval between the intensity column of samples" help="eg, 1 if subsequent column; 2 if every other column"/>
        <param name="enriched" type="select" label="Phospho enrichemnt type">
            <option value="ST">ST</option>
            <option value="Y">Y</option>
        </param>
        <param name="collapse_func" type="select" label="Intensity merge function">
            <option value="sum">sum</option>
            <option value="averge">averge</option>
        </param>
        <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" label="Localization Probability Cutoff"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="phosphopeptide_intensities.tsv"/>
    </outputs>
    <tests>
        <test>
            <param name="phospho_sites" ftype="tabular" value="Phospho (ST)Sites_NancyDu.txt"/>
            <param name="phosphoCol" value="37"/>
            <param name="numSamples" value="6"/>
            <param name="startCol" value="58"/>
            <param name="intervalCol" value="1"/>
            <param name="enriched" value="ST"/>
            <param name="collapse_func" value="sum"/>
            <param name="localProbCutoff" value="0.75"/>
            <output name="output">
                <assert_contents>
                    <has_text text="Phosphopeptide" />
                    <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" />
                    <has_text text="997800000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>