Mercurial > repos > tduigou > rpreport
comparison rpreport.xml @ 0:d09a51507aaf draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
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date | Mon, 14 Feb 2022 14:23:00 +0000 |
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children | 3ea8aa1e94b4 |
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1 <tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09"> | |
2 <description>Generates HTML report to explore the main characteristics of pathways | |
3 predicted with RetroPath suite</description> | |
4 <macros> | |
5 <token name="@TOOL_VERSION@">5.12.1</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($input_type_conditional.input_type) == "sbml": | |
12 cd /tmp && | |
13 #set input_folder="tmp_folder" | |
14 mkdir -p '$input_folder' && | |
15 #for $input in $input_type_conditional.input_sbml.keys(): | |
16 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input'; | |
17 #end for | |
18 python -m rptools.rpreport -d '$input_folder' | |
19 #elif str($input_type_conditional.input_type) == "tar": | |
20 python -m rptools.rpreport '${input_type_conditional.input_tar}' | |
21 #end if | |
22 '$html_file.files_path' | |
23 && cp '$html_file.files_path'/index.html '$html_file' | |
24 ]]></command> | |
25 <inputs> | |
26 <conditional name="input_type_conditional"> | |
27 <param name="input_type" type="select" label="Source SBML format"> | |
28 <option value="tar" selected="True">TAR</option> | |
29 <option value="sbml">Collection</option> | |
30 </param> | |
31 <when value="tar"> | |
32 <param name="input_tar" type="data" format="tar" label="Source SBML" /> | |
33 </when> | |
34 <when value="sbml"> | |
35 <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> | |
36 </when> | |
37 </conditional> | |
38 </inputs> | |
39 <outputs> | |
40 <data name="html_file" format="html" label="Pathways HTML Report"/> | |
41 </outputs> | |
42 <tests> | |
43 <test> | |
44 <!-- test 2: check if identical html output is produced (tar input) --> | |
45 <conditional name="input_type_conditional"> | |
46 <param name="input_type" value="tar"/> | |
47 <param name="input_tar" value="input_rpSBML.tar" /> | |
48 </conditional> | |
49 <output name="html_file" file="rpreport_output.html" compare="diff"/> | |
50 </test> | |
51 </tests> | |
52 <help><![CDATA[ | |
53 rpReport | |
54 ========= | |
55 | |
56 Generates HTML pages to explore the main characteristics (thermodynamics, | |
57 fluxes, number of metabolic steps, reaction rule score) of pathways predicted | |
58 with RetroPath suite | |
59 | |
60 | |
61 Input | |
62 ----- | |
63 | |
64 Required: | |
65 | |
66 * **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s). | |
67 | |
68 Output | |
69 ------ | |
70 * **output_folder**: (string) Output folder where report file(s) will be generated. | |
71 | |
72 Project Links | |
73 --------------------- | |
74 * `GitHub <https://github.com/brsynth/rptools>`_ | |
75 | |
76 Version | |
77 ---------- | |
78 | |
79 5.12.1 | |
80 | |
81 Authors | |
82 ------- | |
83 | |
84 * **Olivier Telle** | |
85 | |
86 Acknowledgments | |
87 --------------- | |
88 | |
89 * Thomas Duigou | |
90 * Joan Hérisson | |
91 | |
92 Licence | |
93 ------- | |
94 | |
95 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ | |
96 ]]></help> | |
97 </tool> |