Mercurial > repos > galaxyp > phosphopeptide_kinase_mapping

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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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56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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1 <tool id="phosphopeptide_kinase_mapping" name="PhosphoPeptide Upstream Kinase Mapping" version="0.1.0" python_template_version="3.5">
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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2 <requirements>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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3 <requirement type="package" version="5.22.0.1">perl</requirement>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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4 </requirements>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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5 <command detect_errors="exit_code"><![CDATA[
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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6 perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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7 -i '$phophopeptide_intensities'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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8 -f '$protein_fasta'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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9 -n '$networkin'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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10 -m '$p_sty_motifs'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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11 -p '$psp_kinase_substrate'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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12 -r '$psp_regulatory_sites'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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13 -P $phospho_type
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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14 -F $merge_function
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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15 -o 'phophopeptides.tsv'
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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16 ]]></command>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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17 <inputs>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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18 <param name="phophopeptide_intensities" type="data" format="tabular" label="Phosphopeptide intensity file"
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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19 help="generate by MaxQuant Phosphopeptide Intensity"/>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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20 <param name="protein_fasta" type="data" format="fasta" label="Protein fasta database" />
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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21 <param name="networkin" type="data" format="tabular" label="NetworKIN file" />
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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22 <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file" />
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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23 <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset" />
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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24 <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites" />
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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25 <param name="phospho_type" type="select" label="phospho type">
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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26 <option value="sty" selected="true">sty</option>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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27 <option value="y">y</option>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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28 </param>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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29 <param name="merge_function" type="select" label="Merge identical phospho site intensities by">
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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30 <option value="sum" selected="true">sum</option>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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31 <option value="average">average</option>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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32 </param>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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33 </inputs>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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34 <outputs>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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35 <data name="output" format="tabular" from_work_dir="phophopeptides.tsv"/>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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36 </outputs>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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37 <help><![CDATA[
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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38 TODO: Fill in help.
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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39 ]]></help>
56658e35798d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/phosphopeptide_kinase_mapping commit d256bec9d43378291734e2b2a93bdbfcc2d83f61"
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40 </tool>