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comparison spring_mcc.xml @ 41:f316caf098a6 draft default tip

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"planemo upload commit 685e1236afde7cf6bb0c9236de06998d2c211dd3"
author guerler
date Mon, 01 Mar 2021 15:02:36 +0000
parents 172398348efd
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40:06337927c198 41:f316caf098a6
1 <tool id="spring_mcc" name="SPRING MCC" version="0.1.0" python_template_version="3.5" license="MIT"> 1 <tool id="spring_mcc" name="SPRING MCC" version="0.1.0" python_template_version="3.5" license="MIT">
2 <description>plot generator</description> 2 <description>plot generator</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.3.2">matplotlib</requirement> 4 <requirement type="package" version="3.3.2">matplotlib</requirement>
5 <requirement type="package" version="1.2.0">pandas</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 7 <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 '$output' 8 python3 '$__tool_directory__/spring_mcc.py' -i '$input' -b '$database' -e '$experiment' -l '$sampling.locations' -ra '$sampling.regiona' -rb '$sampling.regionb' -n '$sampling.negative' -o '$output'
8 ]]></command> 9 ]]></command>
9 <inputs> 10 <inputs>
11 <param name="experiment" type="text" label="Title" help="Experiment title" value="Results"/>
10 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/> 12 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)."/>
11 <conditional name="sampling"> 13 <conditional name="sampling">
12 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs."> 14 <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> 15 <option value="random">Random Sampling</option>
14 <option value="uniprot">Sampling with UniProt Localization</option> 16 <option value="uniprot">Sampling with UniProt Localization</option>
48 <param name="regiona" type="hidden" value="" /> 50 <param name="regiona" type="hidden" value="" />
49 <param name="regionb" type="hidden" value="" /> 51 <param name="regionb" type="hidden" value="" />
50 </when> 52 </when>
51 </conditional> 53 </conditional>
52 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/> 54 <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> 55 </inputs>
67 <outputs> 56 <outputs>
68 <data format="png" name="output" label="SPRING MCC Image" /> 57 <data format="png" name="output" label="SPRING MCC Image" />
69 </outputs> 58 </outputs>
70 <tests> 59 <tests>
71 <test> 60 <test>
72 <param name="input" value="mcc/human_hv1h2.txt" /> 61 <param name="input" value="mcc/human_hv1h2.txt" />
73 <param name="database" value="mcc/biogrid_fret.txt" /> 62 <param name="database" value="mcc/biogrid_fret.txt" />
74 <param name="method" value="FRET" />
75 <output name="output" file="mcc/human_hv1h2.png" /> 63 <output name="output" file="mcc/human_hv1h2.png" />
76 </test> 64 </test>
77 </tests> 65 </tests>
78 <help><![CDATA[ 66 <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 67 This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared