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comparison 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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28:75d1aedc9b3f 29:41353488926c
1 <tool id="spring_roc" name="SPRING ROC" version="0.1.0" python_template_version="3.5">
2 <description>plot generator</description>
3 <requirements>
4 <requirement type="package" version="3.3.3">matplotlib</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python3 '$__tool_directory__/spring_roc.py' -i '$input' -b '$database' -e '$experiment.type' -m '$experiment.method' -t '$throughput' -o '$rocplot'
8 ]]></command>
9 <inputs>
10 <param format="tabular" name="input" type="data" label="Interactions" help="Prediction Input Table with 2-columns containing UniProt Accession codes."/>
11 <param format="tabular" name="database" type="data" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/>
12 <conditional name="experiment">
13 <param name="type" type="select" label="Experimental Type" display="radio" help="Choose a specific experimental system type.">
14 <option value="">Any</option>
15 <option value="physical">Physical</option>
16 <option value="genetic">Genetic</option>
17 </param>
18 <when value="physical">
19 <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name.">
20 <option value="">Any</option>
21 <option value="Affinity Capture">Affinity Capture-Any</option>
22 <option value="Affinity Capture-Luminescence"></option>
23 <option value="Affinity Capture-MS">Affinity Capture-MS</option>
24 <option value="Affinity Capture-RNA">Affinity Capture-RNA</option>
25 <option value="Affinity Capture-Western">Affinity Capture-Western</option>
26 <option value="Biochemical Activity">Biochemical Activity</option>
27 <option value="Co-crystal Structure">Co-crystal Structure</option>
28 <option value="Co-fractionation">Co-fractionation</option>
29 <option value="Co-localization">Co-localization</option>
30 <option value="Co-purification">Co-purification</option>
31 <option value="Far Western">Far Western</option>
32 <option value="FRET">FRET</option>
33 <option value="PCA">PCA</option>
34 <option value="Protein-peptide">Protein-peptide</option>
35 <option value="Protein-RNA">Protein-RNA</option>
36 <option value="Proximity Label-MS">Proximity Label-MS</option>
37 <option value="Reconstituted Complex">Reconstituted Complex</option>
38 <option value="Two-hybrid">Two-hybrid</option>
39 </param>
40 </when>
41 <when value="genetic">
42 <param name="method" type="hidden" value="" />
43 </when>
44 <when value="">
45 <param name="method" type="hidden" value="" />
46 </when>
47 </conditional>
48 <param name="throughput" type="select" label="Experimental Throughput" display="radio" help="Choose the experimental throughput grade.">
49 <option value="">Any</option>
50 <option value="Low Throughput">Low</option>
51 <option value="High Throughput">High</option>
52 </param>
53 </inputs>
54 <outputs>
55 <data format="png" name="rocplot" label="SPRING ROC Image" />
56 </outputs>
57 <tests>
58 <test>
59 <param format="tabular" name="input" value="roc/human_hv1h2.txt" />
60 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
61 <conditional name="experiment">
62 <param name="type" value="physical" />
63 <param name="method" value="Two-hybrid" />
64 </conditional>
65 <output name="output" file="roc/human_hv1h2.png" />
66 </test>
67 </tests>
68 <help><![CDATA[
69 This tool generates a ROC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared
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
71 choosing a specific experimental method.
72 ]]></help>
73 <citations>
74 <citation type="bibtex">
75 @misc{githubhh-suite,
76 author = {Guerler, Govindarajoo, Zhang},
77 year = {2013},
78 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
79 publisher = {ACS Publications},
80 journal = {Journal of Chemical Information and Modeling},
81 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
82 }
83 </citation>
84 </citations>
85 </tool>