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author | guerler |
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date | Fri, 22 Jan 2021 15:50:27 +0000 |
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children | f316caf098a6 |
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<tool id="spring_mcc" name="SPRING MCC" version="0.1.0" python_template_version="3.5" license="MIT"> <description>plot generator</description> <requirements> <requirement type="package" version="3.3.2">matplotlib</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python3 '$__tool_directory__/spring_mcc.py' -i '$input' -b '$database' -m '$method' -l '$sampling.locations' -ra '$sampling.regiona' -rb '$sampling.regionb' -n '$sampling.negative' -o '$output' ]]></command> <inputs> <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/> <conditional name="sampling"> <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs."> <option value="random">Random Sampling</option> <option value="uniprot">Sampling with UniProt Localization</option> <option value="negative">Specify non-interacting pairs</option> </param> <when value="uniprot"> <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." /> <param name="negative" type="hidden" value="" /> <param name="regiona" type="select" label="Choose First Subcellular Location"> <option value="Cell">Cell</option> <option value="Cytoplasm">Cytoplasm</option> <option value="Membrane" selected="True">Membrane</option> <option value="Mitochondrion" selected="True">Mitochondrion</option> <option value="Nucleus">Nucleus</option> <option value="Periplasm">Periplasm</option> <option value="Secreted">Secreted</option> </param> <param name="regionb" type="select" label="Choose Second Subcellular Location"> <option value="Cell">Cell</option> <option value="Cytoplasm">Cytoplasm</option> <option value="Membrane" selected="True">Membrane</option> <option value="Mitochondrion" selected="True">Mitochondrion</option> <option value="Nucleus">Nucleus</option> <option value="Periplasm">Periplasm</option> <option value="Secreted">Secreted</option> </param> </when> <when value="random"> <param name="locations" type="hidden" value="" /> <param name="negative" type="hidden" value="" /> <param name="regiona" type="hidden" value="" /> <param name="regionb" type="hidden" value="" /> </when> <when value="negative"> <param name="locations" type="hidden" value="" /> <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs (2-columns)." /> <param name="regiona" type="hidden" value="" /> <param name="regionb" type="hidden" value="" /> </when> </conditional> <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/> <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name."> <option value="Affinity Capture-MS">Affinity Capture-MS</option> <option value="Biochemical Activity">Biochemical Activity</option> <option value="Co-crystal Structure">Co-crystal Structure</option> <option value="Co-fractionation">Co-fractionation</option> <option value="Co-localization">Co-localization</option> <option value="Co-purification">Co-purification</option> <option value="Far Western">Far Western</option> <option value="FRET">FRET</option> <option value="PCA">PCA</option> <option value="Reconstituted Complex">Reconstituted Complex</option> <option value="Two-hybrid">Two-hybrid</option> </param> </inputs> <outputs> <data format="png" name="output" label="SPRING MCC Image" /> </outputs> <tests> <test> <param name="input" value="mcc/human_hv1h2.txt" /> <param name="database" value="mcc/biogrid_fret.txt" /> <param name="method" value="FRET" /> <output name="output" file="mcc/human_hv1h2.png" /> </test> </tests> <help><![CDATA[ This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared to a given BioGRID database file in TAB 3.0 format. Non-interacting protein pairs are randomly sampled. ]]></help> <citations> <citation type="bibtex"> @misc{githubhh-suite, author = {Guerler, Govindarajoo, Zhang}, year = {2013}, title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction}, publisher = {ACS Publications}, journal = {Journal of Chemical Information and Modeling}, url = {https://pubs.acs.org/doi/10.1021/ci300579r}, } </citation> </citations> </tool>