Mercurial > repos > tduigou > rptools_rpreport

annotate rpreport.xml @ 0:a1764894d6ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Wed, 16 Nov 2022 11:11:58 +0000
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a1764894d6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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1 <tool id="rptools_rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Explore the main characteristics of pathways predicted with RetroPath suite</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 <command detect_errors="exit_code"><![CDATA[
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11 #if str($input_type_conditional.input_type) == "sbml":
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12 #set input_folder="tmp_folder"
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13 mkdir -p '$input_folder' &&
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14 #for $input in $input_type_conditional.input_sbml.keys():
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15 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input' &&
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16 #end for
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17 python -m rptools.rpreport -d '$input_folder'
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18 #elif str($input_type_conditional.input_type) == "tar":
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19 python -m rptools.rpreport '${input_type_conditional.input_tar}'
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20 #end if
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21 '$html_file.files_path'
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22 && cp '$html_file.files_path'/index.html '$html_file'
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23 ]]></command>
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24 <inputs>
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25 <conditional name="input_type_conditional">
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26 <param name="input_type" type="select" label="Source SBML format">
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27 <option value="tar" selected="True">TAR</option>
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28 <option value="sbml">Collection</option>
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29 </param>
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30 <when value="tar">
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31 <param name="input_tar" type="data" format="tar" label="Source SBML" help="rpSBML file(s) containing pathways predicted with RetroPath suite in TAR format"/>
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32 </when>
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33 <when value="sbml">
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34 <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" help="Collection of rpSBML files containing pathways predicted with RetroPath suite"/>
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="html_file" format="html" label="Pathways HTML Report"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <!-- test 1: check if identical html output is produced (tar input) -->
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44 <conditional name="input_type_conditional">
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45 <param name="input_type" value="tar"/>
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46 <param name="input_tar" value="input_rpSBML.tar" />
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47 </conditional>
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48 <output name="html_file" file="rpreport_output.html" compare="diff"/>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 rpReport
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53 =========
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54
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55 Generates HTML pages to explore the main characteristics (thermodynamics,
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56 fluxes, number of metabolic steps, reaction rule score) of pathways predicted
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57 with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
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58
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59
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60 Input
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61 -----
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62
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63 Required:
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64
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65 * **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite.
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66
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67 Output
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68 ------
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69
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70 * **Pathways HTML Report**: Pathways HTML Report
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71
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72 Project Links
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73 ---------------------
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74
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75 * `GitHub <https://github.com/brsynth/rptools>`_
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76
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77 Acknowledgments
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78 ---------------
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79
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80 * Thomas Duigou
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81 * Joan Hérisson
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82
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83 Licence
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84 -------
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85
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86 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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87 ]]></help>
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88 <creator>
a1764894d6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
tduigou
parents:
diff changeset
89 <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" />
a1764894d6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
tduigou
parents:
diff changeset
90 </creator>
a1764894d6ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
tduigou
parents:
diff changeset
91 </tool>