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annotate rpranker.xml @ 2:ebbdb240c507 draft

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planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Fri, 21 Oct 2022 14:57:59 +0000
parents bab690866445
children 422a5c9f3583
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1 <tool id="rpranker" name="Rank Pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Rank heterologous pathways according to their global score</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">5.13.1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="WARNING" level="warning" />
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12 <regex match="ERROR" level="fatal" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 python -m rptools.rprank
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16 --pathways
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17 #for $input in $pathway_collection
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18 '$input'
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19 #end for
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20 > '$sorted_pathways'
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21 ]]></command>
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22 <inputs>
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23 <param name="pathway_collection" type="data_collection" format="sbml" collection_type="list" label="Pathways" />
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24 </inputs>
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25 <outputs>
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26 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <!-- test 1: check if identical outputs are produced with default parameters -->
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31 <param name="pathway_collection" >
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32 <collection type="list">
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33 <element name="rp_003_0261" value="rp_003_0261.xml" />
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34 <element name="rp_003_0131" value="rp_003_0131.xml" />
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35 <element name="rp_003_0001" value="rp_003_0001.xml" />
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36 <element name="rp_002_0021" value="rp_002_0021.xml" />
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37 <element name="rp_002_0011" value="rp_002_0011.xml" />
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38 <element name="rp_002_0001" value="rp_002_0001.xml" />
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39 <element name="rp_001_0011" value="rp_001_0011.xml" />
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40 <element name="rp_001_0006" value="rp_001_0006.xml" />
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41 <element name="rp_001_0001" value="rp_001_0001.xml" />
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42 </collection>
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43 </param>
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44 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 Rank Pathways
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49 ================
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50
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51 Sort a list of pathways according to their global score.
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52
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53 Input
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54 -----
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55
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56 Required:
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57
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58 * **Pathways**\ : List of pathway files (rpSBML)
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59
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60 Output
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61 ------
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62
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63 * **Ranked Pathways**\ : Sorted names and scores of pathways
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64
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65 Project Links
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66 ------------------
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67
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68 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
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69
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70 License
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71 -------
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72
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73 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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74
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75 Acknowledgments
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76 ---------------
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77
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78 * Thomas Duigou
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79
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80 ]]></help>
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81 <creator>
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82 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
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83 </creator>
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84 </tool>