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
date Wed, 16 Nov 2022 11:11:58 +0000
parents
children 432623008c84
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-1:000000000000 0:a1764894d6ca
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>