Mercurial > repos > tduigou > rptools_rpreport
comparison rpreport.xml @ 0:a1764894d6ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author | tduigou |
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date | Wed, 16 Nov 2022 11:11:58 +0000 |
parents | |
children | 432623008c84 |
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1 <tool id="rptools_rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> | |
2 <description>Explore the main characteristics of pathways predicted with RetroPath suite</description> | |
3 <macros> | |
4 <token name="@VERSION_SUFFIX@">0</token> | |
5 <token name="@TOOL_VERSION@">5.13.1</token> | |
6 </macros> | |
7 <requirements> | |
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> | |
9 </requirements> | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 #if str($input_type_conditional.input_type) == "sbml": | |
12 #set input_folder="tmp_folder" | |
13 mkdir -p '$input_folder' && | |
14 #for $input in $input_type_conditional.input_sbml.keys(): | |
15 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input' && | |
16 #end for | |
17 python -m rptools.rpreport -d '$input_folder' | |
18 #elif str($input_type_conditional.input_type) == "tar": | |
19 python -m rptools.rpreport '${input_type_conditional.input_tar}' | |
20 #end if | |
21 '$html_file.files_path' | |
22 && cp '$html_file.files_path'/index.html '$html_file' | |
23 ]]></command> | |
24 <inputs> | |
25 <conditional name="input_type_conditional"> | |
26 <param name="input_type" type="select" label="Source SBML format"> | |
27 <option value="tar" selected="True">TAR</option> | |
28 <option value="sbml">Collection</option> | |
29 </param> | |
30 <when value="tar"> | |
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"/> | |
32 </when> | |
33 <when value="sbml"> | |
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"/> | |
35 </when> | |
36 </conditional> | |
37 </inputs> | |
38 <outputs> | |
39 <data name="html_file" format="html" label="Pathways HTML Report"/> | |
40 </outputs> | |
41 <tests> | |
42 <test> | |
43 <!-- test 1: check if identical html output is produced (tar input) --> | |
44 <conditional name="input_type_conditional"> | |
45 <param name="input_type" value="tar"/> | |
46 <param name="input_tar" value="input_rpSBML.tar" /> | |
47 </conditional> | |
48 <output name="html_file" file="rpreport_output.html" compare="diff"/> | |
49 </test> | |
50 </tests> | |
51 <help><![CDATA[ | |
52 rpReport | |
53 ========= | |
54 | |
55 Generates HTML pages to explore the main characteristics (thermodynamics, | |
56 fluxes, number of metabolic steps, reaction rule score) of pathways predicted | |
57 with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_. | |
58 | |
59 | |
60 Input | |
61 ----- | |
62 | |
63 Required: | |
64 | |
65 * **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite. | |
66 | |
67 Output | |
68 ------ | |
69 | |
70 * **Pathways HTML Report**: Pathways HTML Report | |
71 | |
72 Project Links | |
73 --------------------- | |
74 | |
75 * `GitHub <https://github.com/brsynth/rptools>`_ | |
76 | |
77 Acknowledgments | |
78 --------------- | |
79 | |
80 * Thomas Duigou | |
81 * Joan Hérisson | |
82 | |
83 Licence | |
84 ------- | |
85 | |
86 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ | |
87 ]]></help> | |
88 <creator> | |
89 <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" /> | |
90 </creator> | |
91 </tool> |