comparison spring_mcc.xml @ 39:172398348efd draft

"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"
author guerler
date Fri, 22 Jan 2021 15:50:27 +0000
parents
children f316caf098a6
comparison
equal deleted inserted replaced
38:80a4b98121b6 39:172398348efd
1 <tool id="spring_mcc" name="SPRING MCC" version="0.1.0" python_template_version="3.5" license="MIT">
2 <description>plot generator</description>
3 <requirements>
4 <requirement type="package" version="3.3.2">matplotlib</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 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'
8 ]]></command>
9 <inputs>
10 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/>
11 <conditional name="sampling">
12 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs.">
13 <option value="random">Random Sampling</option>
14 <option value="uniprot">Sampling with UniProt Localization</option>
15 <option value="negative">Specify non-interacting pairs</option>
16 </param>
17 <when value="uniprot">
18 <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." />
19 <param name="negative" type="hidden" value="" />
20 <param name="regiona" type="select" label="Choose First Subcellular Location">
21 <option value="Cell">Cell</option>
22 <option value="Cytoplasm">Cytoplasm</option>
23 <option value="Membrane" selected="True">Membrane</option>
24 <option value="Mitochondrion" selected="True">Mitochondrion</option>
25 <option value="Nucleus">Nucleus</option>
26 <option value="Periplasm">Periplasm</option>
27 <option value="Secreted">Secreted</option>
28 </param>
29 <param name="regionb" type="select" label="Choose Second Subcellular Location">
30 <option value="Cell">Cell</option>
31 <option value="Cytoplasm">Cytoplasm</option>
32 <option value="Membrane" selected="True">Membrane</option>
33 <option value="Mitochondrion" selected="True">Mitochondrion</option>
34 <option value="Nucleus">Nucleus</option>
35 <option value="Periplasm">Periplasm</option>
36 <option value="Secreted">Secreted</option>
37 </param>
38 </when>
39 <when value="random">
40 <param name="locations" type="hidden" value="" />
41 <param name="negative" type="hidden" value="" />
42 <param name="regiona" type="hidden" value="" />
43 <param name="regionb" type="hidden" value="" />
44 </when>
45 <when value="negative">
46 <param name="locations" type="hidden" value="" />
47 <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs (2-columns)." />
48 <param name="regiona" type="hidden" value="" />
49 <param name="regionb" type="hidden" value="" />
50 </when>
51 </conditional>
52 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/>
53 <param name="method" type="select" label="Experimental Method" help="Choose a specific experimental method name.">
54 <option value="Affinity Capture-MS">Affinity Capture-MS</option>
55 <option value="Biochemical Activity">Biochemical Activity</option>
56 <option value="Co-crystal Structure">Co-crystal Structure</option>
57 <option value="Co-fractionation">Co-fractionation</option>
58 <option value="Co-localization">Co-localization</option>
59 <option value="Co-purification">Co-purification</option>
60 <option value="Far Western">Far Western</option>
61 <option value="FRET">FRET</option>
62 <option value="PCA">PCA</option>
63 <option value="Reconstituted Complex">Reconstituted Complex</option>
64 <option value="Two-hybrid">Two-hybrid</option>
65 </param>
66 </inputs>
67 <outputs>
68 <data format="png" name="output" label="SPRING MCC Image" />
69 </outputs>
70 <tests>
71 <test>
72 <param name="input" value="mcc/human_hv1h2.txt" />
73 <param name="database" value="mcc/biogrid_fret.txt" />
74 <param name="method" value="FRET" />
75 <output name="output" file="mcc/human_hv1h2.png" />
76 </test>
77 </tests>
78 <help><![CDATA[
79 This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared
80 to a given BioGRID database file in TAB 3.0 format. Non-interacting protein pairs are randomly sampled.
81 ]]></help>
82 <citations>
83 <citation type="bibtex">
84 @misc{githubhh-suite,
85 author = {Guerler, Govindarajoo, Zhang},
86 year = {2013},
87 title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
88 publisher = {ACS Publications},
89 journal = {Journal of Chemical Information and Modeling},
90 url = {https://pubs.acs.org/doi/10.1021/ci300579r},
91 }
92 </citation>
93 </citations>
94 </tool>