Mercurial > repos > guerler > spring_mcc

annotate spring_mcc.xml @ 0:c3e9ffb4c98a draft

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"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author guerler
date Tue, 23 Mar 2021 13:56:55 +0000
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1 <tool id="spring_mcc" name="SPRING MCC" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>plot generator</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 spring_mcc.py
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9 -i '$input'
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10 -b '$database'
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11 -e '$experiment'
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12 -l '$sampling.locations'
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13 -ra '$sampling.regiona'
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14 -rb '$sampling.regionb'
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15 -n '$sampling.negative'
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16 -o '$output'
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17 ]]> </command>
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18 <inputs>
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19 <param name="experiment" type="text" label="Title" help="Experiment title" value="Results" />
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20 <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)." />
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21 <conditional name="sampling">
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22 <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs.">
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23 <option value="random">Random Sampling</option>
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24 <option value="uniprot">Sampling with UniProt Localization</option>
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25 <option value="negative">Specify non-interacting pairs</option>
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26 </param>
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27 <when value="uniprot">
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28 <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." />
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29 <param name="negative" type="hidden" value="" />
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30 <param name="regiona" type="select" label="Choose First Subcellular Location">
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31 <option value="Cell">Cell</option>
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32 <option value="Cytoplasm">Cytoplasm</option>
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33 <option value="Membrane" selected="True">Membrane</option>
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34 <option value="Mitochondrion" selected="True">Mitochondrion</option>
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35 <option value="Nucleus">Nucleus</option>
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36 <option value="Periplasm">Periplasm</option>
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37 <option value="Secreted">Secreted</option>
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38 </param>
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39 <param name="regionb" type="select" label="Choose Second Subcellular Location">
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40 <option value="Cell">Cell</option>
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41 <option value="Cytoplasm">Cytoplasm</option>
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42 <option value="Membrane" selected="True">Membrane</option>
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43 <option value="Mitochondrion" selected="True">Mitochondrion</option>
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44 <option value="Nucleus">Nucleus</option>
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45 <option value="Periplasm">Periplasm</option>
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46 <option value="Secreted">Secreted</option>
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47 </param>
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48 </when>
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49 <when value="random">
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50 <param name="locations" type="hidden" value="" />
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51 <param name="negative" type="hidden" value="" />
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52 <param name="regiona" type="hidden" value="" />
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53 <param name="regionb" type="hidden" value="" />
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54 </when>
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55 <when value="negative">
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56 <param name="locations" type="hidden" value="" />
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57 <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs (2-columns)." />
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58 <param name="regiona" type="hidden" value="" />
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59 <param name="regionb" type="hidden" value="" />
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60 </when>
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61 </conditional>
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62 <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format." />
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63 </inputs>
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64 <outputs>
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65 <data format="png" name="output" label="SPRING MCC Image" />
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="input" value="mcc/human_hv1h2.txt" />
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70 <param name="database" value="mcc/biogrid_fret.txt" />
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71 <output name="output" file="mcc/human_hv1h2.png" compare="sim_size" />
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75
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76 **What it does**
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77
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78 This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared
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79 to a given BioGRID database file in TAB 3.0 format. Non-interacting protein pairs are randomly sampled.
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80
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81 ]]> </help>
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82 <expand macro="citations" />
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83 </tool>