annotate spring_roc.xml @ 36:2fe8ffff530d draft

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date Tue, 24 Nov 2020 18:16:01 +0000
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1 <tool id="spring_roc" name="SPRING ROC" version="0.1.0" python_template_version="3.5" license="MIT">
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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' -l '$sampling.locations' -r '$sampling.regions' -n '$sampling.negative' -o '$rocplot'
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8 ]]></command>
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9 <inputs>
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10 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/>
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11 <conditional name="sampling">
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12 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs.">
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13 <option value="random">Random Sampling</option>
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14 <option value="uniprot">Sampling with UniProt Localization</option>
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15 <option value="negative">Specify non-interacting pairs</option>
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16 </param>
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17 <when value="uniprot">
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18 <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." />
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19 <param name="negative" type="hidden" value="" />
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20 <param name="regions" type="select" multiple="True" label="Choose Subcellular Locations">
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21 <option value="Membrane" selected="True">Membrane</option>
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22 <option value="Mitochondrion" selected="True">Mitochondrion</option>
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23 <option value="Nucleus">Nucleus</option>
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24 <option value="Secreted">Secreted</option>
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25 </param>
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26 </when>
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27 <when value="random">
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28 <param name="negative" type="hidden" value="" />
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29 <param name="locations" type="hidden" value="" />
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30 <param name="regions" type="hidden" value="" />
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31 </when>
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32 <when value="negative">
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33 <param name="locations" type="hidden" value="" />
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34 <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs (2-columns)." />
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35 <param name="regions" type="hidden" value="" />
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36 </when>
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37 </conditional>
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38 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/>
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39 <conditional name="experiment">
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40 <param name="type" type="select" label="Experimental Type" display="radio" help="Choose a specific experimental system type.">
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41 <option value="">Any</option>
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42 <option value="physical">Physical</option>
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43 <option value="genetic">Genetic</option>
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44 </param>
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45 <when value="physical">
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46 <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name.">
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47 <option value="">Any</option>
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48 <option value="Affinity Capture">Affinity Capture-Any</option>
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49 <option value="Affinity Capture-Luminescence"></option>
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50 <option value="Affinity Capture-MS">Affinity Capture-MS</option>
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51 <option value="Affinity Capture-RNA">Affinity Capture-RNA</option>
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52 <option value="Affinity Capture-Western">Affinity Capture-Western</option>
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53 <option value="Biochemical Activity">Biochemical Activity</option>
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54 <option value="Co-crystal Structure">Co-crystal Structure</option>
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55 <option value="Co-fractionation">Co-fractionation</option>
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56 <option value="Co-localization">Co-localization</option>
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57 <option value="Co-purification">Co-purification</option>
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58 <option value="Far Western">Far Western</option>
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59 <option value="FRET">FRET</option>
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60 <option value="PCA">PCA</option>
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61 <option value="Protein-peptide">Protein-peptide</option>
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62 <option value="Protein-RNA">Protein-RNA</option>
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63 <option value="Proximity Label-MS">Proximity Label-MS</option>
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64 <option value="Reconstituted Complex">Reconstituted Complex</option>
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65 <option value="Two-hybrid">Two-hybrid</option>
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66 </param>
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67 </when>
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68 <when value="genetic">
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69 <param name="method" type="hidden" value="" />
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70 </when>
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71 <when value="">
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72 <param name="method" type="hidden" value="" />
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73 </when>
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74 </conditional>
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75 <param name="throughput" type="select" label="Experimental Throughput" display="radio" help="Choose the experimental throughput grade.">
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76 <option value="">Any</option>
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77 <option value="Low Throughput">Low</option>
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78 <option value="High Throughput">High</option>
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79 </param>
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80 </inputs>
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81 <outputs>
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82 <data format="png" name="rocplot" label="SPRING ROC Image" />
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param format="tabular" name="input" value="roc/human_hv1h2.txt" />
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87 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
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88 <output name="output" file="roc/human_hv1h2.png" />
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92 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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93 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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94 choosing a specific experimental method.
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95 ]]></help>
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96 <citations>
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97 <citation type="bibtex">
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98 @misc{githubhh-suite,
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99 author = {Guerler, Govindarajoo, Zhang},
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100 year = {2013},
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101 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
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102 publisher = {ACS Publications},
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103 journal = {Journal of Chemical Information and Modeling},
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104 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
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105 }
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106 </citation>
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107 </citations>
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108 </tool>