Mercurial > repos > tduigou > rpreport
annotate rpreport.xml @ 0:d09a51507aaf draft
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author | tduigou |
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date | Mon, 14 Feb 2022 14:23:00 +0000 |
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children | 3ea8aa1e94b4 |
rev | line source |
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0
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1 <tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09"> |
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2 <description>Generates HTML report to explore the main characteristics of pathways |
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3 predicted with RetroPath suite</description> |
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4 <macros> |
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5 <token name="@TOOL_VERSION@">5.12.1</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($input_type_conditional.input_type) == "sbml": |
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12 cd /tmp && |
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13 #set input_folder="tmp_folder" |
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14 mkdir -p '$input_folder' && |
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15 #for $input in $input_type_conditional.input_sbml.keys(): |
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16 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input'; |
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17 #end for |
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18 python -m rptools.rpreport -d '$input_folder' |
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19 #elif str($input_type_conditional.input_type) == "tar": |
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20 python -m rptools.rpreport '${input_type_conditional.input_tar}' |
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21 #end if |
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22 '$html_file.files_path' |
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23 && cp '$html_file.files_path'/index.html '$html_file' |
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24 ]]></command> |
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25 <inputs> |
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26 <conditional name="input_type_conditional"> |
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27 <param name="input_type" type="select" label="Source SBML format"> |
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28 <option value="tar" selected="True">TAR</option> |
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29 <option value="sbml">Collection</option> |
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30 </param> |
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31 <when value="tar"> |
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32 <param name="input_tar" type="data" format="tar" label="Source SBML" /> |
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33 </when> |
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34 <when value="sbml"> |
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35 <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> |
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36 </when> |
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37 </conditional> |
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38 </inputs> |
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39 <outputs> |
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40 <data name="html_file" format="html" label="Pathways HTML Report"/> |
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41 </outputs> |
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42 <tests> |
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43 <test> |
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44 <!-- test 2: check if identical html output is produced (tar input) --> |
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45 <conditional name="input_type_conditional"> |
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46 <param name="input_type" value="tar"/> |
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47 <param name="input_tar" value="input_rpSBML.tar" /> |
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48 </conditional> |
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49 <output name="html_file" file="rpreport_output.html" compare="diff"/> |
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50 </test> |
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51 </tests> |
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52 <help><![CDATA[ |
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53 rpReport |
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54 ========= |
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55 |
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56 Generates HTML pages to explore the main characteristics (thermodynamics, |
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57 fluxes, number of metabolic steps, reaction rule score) of pathways predicted |
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58 with RetroPath suite |
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59 |
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60 |
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61 Input |
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62 ----- |
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63 |
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64 Required: |
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65 |
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66 * **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s). |
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67 |
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68 Output |
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69 ------ |
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70 * **output_folder**: (string) Output folder where report file(s) will be generated. |
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71 |
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72 Project Links |
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73 --------------------- |
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74 * `GitHub <https://github.com/brsynth/rptools>`_ |
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75 |
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76 Version |
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77 ---------- |
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78 |
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79 5.12.1 |
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80 |
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81 Authors |
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82 ------- |
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83 |
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84 * **Olivier Telle** |
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85 |
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86 Acknowledgments |
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87 --------------- |
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88 |
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89 * Thomas Duigou |
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90 * Joan Hérisson |
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91 |
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92 Licence |
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93 ------- |
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94 |
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95 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ |
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96 ]]></help> |
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97 </tool> |