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author tduigou
date Fri, 18 Nov 2022 16:02:09 +0000
parents 3057fc312ff1
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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@">6.0.1</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 #for $file in $pathway_collection
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16 ln -s $file $file.name &&
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17 #end for
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18
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19 python -m rptools.rprank
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20 --pathways
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21
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22 #for $file in $pathway_collection
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23 $file.name
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24 #end for
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25
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26 > '$sorted_pathways'
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27 ]]></command>
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28 <inputs>
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29 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
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30 </inputs>
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31 <outputs>
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32 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <!-- test 1: check if identical outputs are produced with default parameters -->
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37 <param name="pathway_collection" value="rp_003_0261.xml,rp_003_0131.xml,rp_003_0001.xml,rp_002_0021.xml,rp_002_0011.xml,rp_002_0001.xml,rp_001_0011.xml,rp_001_0006.xml,rp_001_0001.xml"/>
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38 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 Rank Pathways
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43 ================
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44
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45 Sort a list of pathways according to their global score.
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46
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47 Input
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48 -----
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49
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50 Required:
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51
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52 * **Pathways**\ : List of pathway files (rpSBML)
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53
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54 Output
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55 ------
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56
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57 * **Ranked Pathways**\ : Sorted names and scores of pathways
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58
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59 Project Links
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60 ------------------
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61
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62 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
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63
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64 License
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65 -------
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66
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67 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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68
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69 Acknowledgments
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70 ---------------
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71
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72 * Thomas Duigou
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73
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74 ]]></help>
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75 <creator>
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76 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
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77 </creator>
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78 </tool>