annotate spring_roc.xml @ 32:11b3fc8b5b48 draft

"planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
author guerler
date Tue, 24 Nov 2020 17:26:23 +0000
parents 3071750405c9
children f115fbf3ac63
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
30
b0e195a47df7 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7"
guerler
parents: 29
diff changeset
1 <tool id="spring_roc" name="SPRING ROC" version="0.1.0" python_template_version="3.5" license="MIT">
29
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
2 <description>plot generator</description>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
3 <requirements>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
4 <requirement type="package" version="3.3.3">matplotlib</requirement>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
5 </requirements>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
31
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
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' -o '$rocplot'
29
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
8 ]]></command>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
9 <inputs>
31
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
10 <param name="input" type="data" format="tabular" label="Interactions" help="Prediction Input Table with 2-columns containing UniProt Accession codes."/>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
11 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
12 <conditional name="sampling">
32
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
13 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Decide how to retrieve non-interacting pairs.">
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
14 <option value="random">Random Sampling</option>
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
15 <option value="uniprot">Sampling with UniProt Localization</option>
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
16 </param>
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
17 <when value="uniprot">
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
18 <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." optional="True" />
31
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
19 <param name="regions" type="select" multiple="True" label="Choose Subcelluar Locations">
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
20 <option value="Membrane" selected="True">Membrane</option>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
21 <option value="Mitochondrion" selected="True">Mitochondrion</option>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
22 <option value="Nucleus">Nucleus</option>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
23 <option value="Secreted">Secreted</option>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
24 </param>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
25 </when>
32
11b3fc8b5b48 "planemo upload commit 90edad77d24453810d6792eaf54ae2ce2ee0913f-dirty"
guerler
parents: 31
diff changeset
26 <when value="random">
31
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
27 <param name="locations" type="hidden" value="" />
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
28 <param name="regions" type="hidden" value="" />
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
29 </when>
3071750405c9 "planemo upload commit b306c715d8284c097220bc5c8461399fdc05eac7-dirty"
guerler
parents: 30
diff changeset
30 </conditional>
29
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
31 <conditional name="experiment">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
32 <param name="type" type="select" label="Experimental Type" display="radio" help="Choose a specific experimental system type.">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
33 <option value="">Any</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
34 <option value="physical">Physical</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
35 <option value="genetic">Genetic</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
36 </param>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
37 <when value="physical">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
38 <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name.">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
39 <option value="">Any</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
40 <option value="Affinity Capture">Affinity Capture-Any</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
41 <option value="Affinity Capture-Luminescence"></option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
42 <option value="Affinity Capture-MS">Affinity Capture-MS</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
43 <option value="Affinity Capture-RNA">Affinity Capture-RNA</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
44 <option value="Affinity Capture-Western">Affinity Capture-Western</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
45 <option value="Biochemical Activity">Biochemical Activity</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
46 <option value="Co-crystal Structure">Co-crystal Structure</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
47 <option value="Co-fractionation">Co-fractionation</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
48 <option value="Co-localization">Co-localization</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
49 <option value="Co-purification">Co-purification</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
50 <option value="Far Western">Far Western</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
51 <option value="FRET">FRET</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
52 <option value="PCA">PCA</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
53 <option value="Protein-peptide">Protein-peptide</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
54 <option value="Protein-RNA">Protein-RNA</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
55 <option value="Proximity Label-MS">Proximity Label-MS</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
56 <option value="Reconstituted Complex">Reconstituted Complex</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
57 <option value="Two-hybrid">Two-hybrid</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
58 </param>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
59 </when>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
60 <when value="genetic">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
61 <param name="method" type="hidden" value="" />
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
62 </when>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
63 <when value="">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
64 <param name="method" type="hidden" value="" />
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
65 </when>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
66 </conditional>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
67 <param name="throughput" type="select" label="Experimental Throughput" display="radio" help="Choose the experimental throughput grade.">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
68 <option value="">Any</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
69 <option value="Low Throughput">Low</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
70 <option value="High Throughput">High</option>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
71 </param>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
72 </inputs>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
73 <outputs>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
74 <data format="png" name="rocplot" label="SPRING ROC Image" />
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
75 </outputs>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
76 <tests>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
77 <test>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
78 <param format="tabular" name="input" value="roc/human_hv1h2.txt" />
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
79 <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
80 <output name="output" file="roc/human_hv1h2.png" />
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
81 </test>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
82 </tests>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
83 <help><![CDATA[
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
84 This tool generates a ROC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
85 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
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
86 choosing a specific experimental method.
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
87 ]]></help>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
88 <citations>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
89 <citation type="bibtex">
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
90 @misc{githubhh-suite,
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
91 author = {Guerler, Govindarajoo, Zhang},
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
92 year = {2013},
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
93 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
94 publisher = {ACS Publications},
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
95 journal = {Journal of Chemical Information and Modeling},
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
96 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
97 }
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
98 </citation>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
99 </citations>
41353488926c "planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"
guerler
parents:
diff changeset
100 </tool>