Mercurial > repos > tduigou > rpranker

annotate rpranker.xml @ 3:422a5c9f3583 draft

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planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Mon, 24 Oct 2022 10:14:47 +0000
parents ebbdb240c507
children 0b6c315489e4
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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 #set files = '" "'.join([str($file) for $file in $pathway_collection])
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18 "${files}"
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19 > '$sorted_pathways'
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20 ]]></command>
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21 <inputs>
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22 <param name="pathway_collection" type="data" format="sbml" multiple="true" min="2" label="Pathways" />
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23 </inputs>
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24 <outputs>
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25 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <!-- test 1: check if identical outputs are produced with default parameters -->
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30 <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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31 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 Rank Pathways
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36 ================
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37
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38 Sort a list of pathways according to their global score.
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39
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40 Input
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41 -----
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42
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43 Required:
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44
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45 * **Pathways**\ : List of pathway files (rpSBML)
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46
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47 Output
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48 ------
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49
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50 * **Ranked Pathways**\ : Sorted names and scores of pathways
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51
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52 Project Links
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53 ------------------
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54
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55 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
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56
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57 License
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58 -------
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59
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60 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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61
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62 Acknowledgments
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63 ---------------
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64
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65 * Thomas Duigou
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66
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67 ]]></help>
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68 <creator>
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69 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
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70 </creator>
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71 </tool>