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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
author galaxyp
date Thu, 04 Nov 2021 19:37:36 +0000
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<tool id="phosphopeptide_kinase_mapping" name="PhosphoPeptide Upstream Kinase Mapping" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="5.22.0.1">perl</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
        -i '$phophopeptide_intensities'
        -f '$protein_fasta'
        -n '$networkin'
        -m '$p_sty_motifs'
        -p '$psp_kinase_substrate'
        -r '$psp_regulatory_sites'
        -P $phospho_type
        -F $merge_function
        -o 'phophopeptides.tsv'
    ]]></command>
    <inputs>
        <param name="phophopeptide_intensities" type="data" format="tabular" label="Phosphopeptide intensity file" 
            help="generate by MaxQuant Phosphopeptide Intensity"/>
        <param name="protein_fasta" type="data" format="fasta" label="Protein fasta database" />
        <param name="networkin" type="data" format="tabular" label="NetworKIN file" />
        <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file" />
        <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset" />
        <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites" />
        <param name="phospho_type" type="select" label="phospho type">
            <option value="sty" selected="true">sty</option>
            <option value="y">y</option>
        </param>
        <param name="merge_function" type="select" label="Merge identical phospho site intensities by">
            <option value="sum" selected="true">sum</option>
            <option value="average">average</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="phophopeptides.tsv"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>