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annotate rpranker.xml @ 0:e95370d2e5f9 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 18:19:24 +0000
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1 <tool id="rpranker" name="Rank Pathways" version="5.10.0">
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2 <description>Rank heterologous pathways according to their global score</description>
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3 <requirements>
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4 <requirement type="package" version="5.10.0">rptools</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="WARNING" level="warning" />
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8 <regex match="ERROR" level="fatal" />
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python -m rptools.rprank
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12 --pathways
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13 #for $input in $pathway_collection
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14 '$input'
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15 #end for
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16 > '$sorted_pathways'
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17 ]]></command>
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18 <inputs>
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19 <param name="pathway_collection" type="data_collection" collection_type="list" label="Pathways" />
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20 </inputs>
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21 <outputs>
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22 <data name="sorted_pathways" format="csv" label="Ranked Pathways" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <!-- test 1: check if identical outputs are produced with default parameters -->
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27 <param name="pathway_collection" >
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28 <collection type="list">
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29 <element name="rp_003_0261" value="rp_003_0261.xml" />
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30 <element name="rp_003_0131" value="rp_003_0131.xml" />
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31 <element name="rp_003_0001" value="rp_003_0001.xml" />
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32 <element name="rp_002_0021" value="rp_002_0021.xml" />
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33 <element name="rp_002_0011" value="rp_002_0011.xml" />
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34 <element name="rp_002_0001" value="rp_002_0001.xml" />
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35 <element name="rp_001_0011" value="rp_001_0011.xml" />
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36 <element name="rp_001_0006" value="rp_001_0006.xml" />
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37 <element name="rp_001_0001" value="rp_001_0001.xml" />
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38 </collection>
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39 </param>
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40 <output name="sorted_pathways" file="lycopene_ranked_pathways.csv" ftype="csv" compare="diff" sort="true" />
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 Rank Pathways
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45 ================
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46
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47 Sort a list of pathways according to their global score.
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48
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49 Input
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50 -----
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51
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52 Required:
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53
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54 * **pathways**\ : (list of string) Paths to pathway (rpSBML) files
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55
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56 Output
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57 ------
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58
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59 * **output**\ : (string) Sorted names and scores of pathways
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60
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61 Project Links
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62 ------------------
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63
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64 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rprank>`_
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65
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66 Version
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67 ----------
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68
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69 5.10.0
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70
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71 License
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72 -------
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73
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74 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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75
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76 Authors
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77 -------
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78
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79 * **Joan Hérisson**
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80
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81 Acknowledgments
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82 ---------------
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83
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84 * Thomas Duigou
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85
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86 ]]></help>
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87 </tool>