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annotate spring_roc.xml @ 29:41353488926c draft

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"planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
author guerler
date Sun, 22 Nov 2020 14:15:24 +0000
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1 <tool id="spring_roc" name="SPRING ROC" version="0.1.0" python_template_version="3.5">
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2 <description>plot generator</description>
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3 <requirements>
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4 <requirement type="package" version="3.3.3">matplotlib</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python3 '$__tool_directory__/spring_roc.py' -i '$input' -b '$database' -e '$experiment.type' -m '$experiment.method' -t '$throughput' -o '$rocplot'
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8 ]]></command>
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9 <inputs>
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10 <param format="tabular" name="input" type="data" label="Interactions" help="Prediction Input Table with 2-columns containing UniProt Accession codes."/>
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11 <param format="tabular" name="database" type="data" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/>
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12 <conditional name="experiment">
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13 <param name="type" type="select" label="Experimental Type" display="radio" help="Choose a specific experimental system type.">
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14 <option value="">Any</option>
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15 <option value="physical">Physical</option>
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16 <option value="genetic">Genetic</option>
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17 </param>
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18 <when value="physical">
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19 <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name.">
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20 <option value="">Any</option>
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21 <option value="Affinity Capture">Affinity Capture-Any</option>
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22 <option value="Affinity Capture-Luminescence"></option>
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23 <option value="Affinity Capture-MS">Affinity Capture-MS</option>
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24 <option value="Affinity Capture-RNA">Affinity Capture-RNA</option>
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25 <option value="Affinity Capture-Western">Affinity Capture-Western</option>
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26 <option value="Biochemical Activity">Biochemical Activity</option>
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27 <option value="Co-crystal Structure">Co-crystal Structure</option>
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28 <option value="Co-fractionation">Co-fractionation</option>
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29 <option value="Co-localization">Co-localization</option>
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30 <option value="Co-purification">Co-purification</option>
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31 <option value="Far Western">Far Western</option>
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32 <option value="FRET">FRET</option>
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33 <option value="PCA">PCA</option>
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34 <option value="Protein-peptide">Protein-peptide</option>
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35 <option value="Protein-RNA">Protein-RNA</option>
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36 <option value="Proximity Label-MS">Proximity Label-MS</option>
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37 <option value="Reconstituted Complex">Reconstituted Complex</option>
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38 <option value="Two-hybrid">Two-hybrid</option>
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39 </param>
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40 </when>
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41 <when value="genetic">
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42 <param name="method" type="hidden" value="" />
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43 </when>
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44 <when value="">
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45 <param name="method" type="hidden" value="" />
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46 </when>
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47 </conditional>
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48 <param name="throughput" type="select" label="Experimental Throughput" display="radio" help="Choose the experimental throughput grade.">
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49 <option value="">Any</option>
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50 <option value="Low Throughput">Low</option>
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51 <option value="High Throughput">High</option>
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52 </param>
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53 </inputs>
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54 <outputs>
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55 <data format="png" name="rocplot" label="SPRING ROC Image" />
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param format="tabular" name="input" value="roc/human_hv1h2.txt" />
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60 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
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61 <conditional name="experiment">
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62 <param name="type" value="physical" />
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63 <param name="method" value="Two-hybrid" />
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64 </conditional>
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65 <output name="output" file="roc/human_hv1h2.png" />
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 This tool generates a ROC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared
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70 to a given BioGRID database file in TAB 3.0 format. Non-interacting protein pairs are randomly sampled. Optionally, users may filter the BioGRID database by
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71 choosing a specific experimental method.
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72 ]]></help>
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73 <citations>
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74 <citation type="bibtex">
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75 @misc{githubhh-suite,
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76 author = {Guerler, Govindarajoo, Zhang},
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77 year = {2013},
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78 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
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79 publisher = {ACS Publications},
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80 journal = {Journal of Chemical Information and Modeling},
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81 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
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82 }
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83 </citation>
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84 </citations>
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85 </tool>