Mercurial > repos > tduigou > rpranker
annotate rpranker.xml @ 3:422a5c9f3583 draft
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author | tduigou |
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date | Mon, 24 Oct 2022 10:14:47 +0000 |
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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> |