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comparison spring_roc.xml @ 34:b300ddbbf9d0 draft

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"planemo upload commit 0410e2fadc4e9fc1df6010de7b3678154cbdfe62-dirty"
author guerler
date Tue, 24 Nov 2020 17:55:07 +0000
parents f115fbf3ac63
children 2fe8ffff530d
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33:f115fbf3ac63 34:b300ddbbf9d0
2 <description>plot generator</description> 2 <description>plot generator</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.3.3">matplotlib</requirement> 4 <requirement type="package" version="3.3.3">matplotlib</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 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' -l '$sampling.locations' -r '$sampling.regions' -o '$rocplot' 7 python3 '$__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'
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param name="input" type="data" format="tabular" label="Interactions" help="Prediction Input Table with 2-columns containing UniProt Accession codes."/> 10 <param name="input" type="data" format="tabular" label="Interactions" help="Prediction Input Table with 2-columns containing UniProt Accession codes."/>
11 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/> 11 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format."/>
12 <conditional name="sampling"> 12 <conditional name="sampling">
13 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Decide how to retrieve non-interacting pairs."> 13 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Decide how to retrieve non-interacting pairs.">
14 <option value="random">Random Sampling</option> 14 <option value="random">Random Sampling</option>
15 <option value="uniprot">Sampling with UniProt Localization</option> 15 <option value="uniprot">Sampling with UniProt Localization</option>
16 <option value="negative">Specify non-interacting pairs</option>
16 </param> 17 </param>
17 <when value="uniprot"> 18 <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." optional="True" /> 19 <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." />
20 <param name="negative" type="hidden" value="" />
19 <param name="regions" type="select" multiple="True" label="Choose Subcellular Locations"> 21 <param name="regions" type="select" multiple="True" label="Choose Subcellular Locations">
20 <option value="Membrane" selected="True">Membrane</option> 22 <option value="Membrane" selected="True">Membrane</option>
21 <option value="Mitochondrion" selected="True">Mitochondrion</option> 23 <option value="Mitochondrion" selected="True">Mitochondrion</option>
22 <option value="Nucleus">Nucleus</option> 24 <option value="Nucleus">Nucleus</option>
23 <option value="Secreted">Secreted</option> 25 <option value="Secreted">Secreted</option>
24 </param> 26 </param>
25 </when> 27 </when>
26 <when value="random"> 28 <when value="random">
29 <param name="negative" type="hidden" value="" />
27 <param name="locations" type="hidden" value="" /> 30 <param name="locations" type="hidden" value="" />
31 <param name="regions" type="hidden" value="" />
32 </when>
33 <when value="negative">
34 <param name="locations" type="hidden" value="" />
35 <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs." />
28 <param name="regions" type="hidden" value="" /> 36 <param name="regions" type="hidden" value="" />
29 </when> 37 </when>
30 </conditional> 38 </conditional>
31 <conditional name="experiment"> 39 <conditional name="experiment">
32 <param name="type" type="select" label="Experimental Type" display="radio" help="Choose a specific experimental system type."> 40 <param name="type" type="select" label="Experimental Type" display="radio" help="Choose a specific experimental system type.">