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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:32:44 +0000
parents d09a51507aaf
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0:d09a51507aaf 1:3ea8aa1e94b4
1 <tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Generates HTML report to explore the main characteristics of pathways 2 <description>Explore the main characteristics of pathways predicted with RetroPath suite</description>
3 predicted with RetroPath suite</description>
4 <macros> 3 <macros>
5 <token name="@TOOL_VERSION@">5.12.1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">6.0.1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #if str($input_type_conditional.input_type) == "sbml": 11 #if str($input_type_conditional.input_type) == "sbml":
12 cd /tmp &&
13 #set input_folder="tmp_folder" 12 #set input_folder="tmp_folder"
14 mkdir -p '$input_folder' && 13 mkdir -p '$input_folder' &&
15 #for $input in $input_type_conditional.input_sbml.keys(): 14 #for $input in $input_type_conditional.input_sbml.keys():
16 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input'; 15 ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input' &&
17 #end for 16 #end for
18 python -m rptools.rpreport -d '$input_folder' 17 python -m rptools.rpreport -d '$input_folder'
19 #elif str($input_type_conditional.input_type) == "tar": 18 #elif str($input_type_conditional.input_type) == "tar":
20 python -m rptools.rpreport '${input_type_conditional.input_tar}' 19 python -m rptools.rpreport '${input_type_conditional.input_tar}'
21 #end if 20 #end if
27 <param name="input_type" type="select" label="Source SBML format"> 26 <param name="input_type" type="select" label="Source SBML format">
28 <option value="tar" selected="True">TAR</option> 27 <option value="tar" selected="True">TAR</option>
29 <option value="sbml">Collection</option> 28 <option value="sbml">Collection</option>
30 </param> 29 </param>
31 <when value="tar"> 30 <when value="tar">
32 <param name="input_tar" type="data" format="tar" label="Source SBML" /> 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"/>
33 </when> 32 </when>
34 <when value="sbml"> 33 <when value="sbml">
35 <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source 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"/>
36 </when> 35 </when>
37 </conditional> 36 </conditional>
38 </inputs> 37 </inputs>
39 <outputs> 38 <outputs>
40 <data name="html_file" format="html" label="Pathways HTML Report"/> 39 <data name="html_file" format="html" label="Pathways HTML Report"/>
41 </outputs> 40 </outputs>
42 <tests> 41 <tests>
43 <test> 42 <test>
44 <!-- test 2: check if identical html output is produced (tar input) --> 43 <!-- test 1: check if identical html output is produced (tar input) -->
45 <conditional name="input_type_conditional"> 44 <conditional name="input_type_conditional">
46 <param name="input_type" value="tar"/> 45 <param name="input_type" value="tar"/>
47 <param name="input_tar" value="input_rpSBML.tar" /> 46 <param name="input_tar" value="input_rpSBML.tar" />
48 </conditional> 47 </conditional>
49 <output name="html_file" file="rpreport_output.html" compare="diff"/> 48 <output name="html_file" file="rpreport_output.html" compare="diff"/>
53 rpReport 52 rpReport
54 ========= 53 =========
55 54
56 Generates HTML pages to explore the main characteristics (thermodynamics, 55 Generates HTML pages to explore the main characteristics (thermodynamics,
57 fluxes, number of metabolic steps, reaction rule score) of pathways predicted 56 fluxes, number of metabolic steps, reaction rule score) of pathways predicted
58 with RetroPath suite 57 with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
59 58
60 59
61 Input 60 Input
62 ----- 61 -----
63 62
64 Required: 63 Required:
65 64
66 * **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s). 65 * **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite.
67 66
68 Output 67 Output
69 ------ 68 ------
70 * **output_folder**: (string) Output folder where report file(s) will be generated. 69
70 * **Pathways HTML Report**: Pathways HTML Report
71 71
72 Project Links 72 Project Links
73 --------------------- 73 ---------------------
74
74 * `GitHub <https://github.com/brsynth/rptools>`_ 75 * `GitHub <https://github.com/brsynth/rptools>`_
75
76 Version
77 ----------
78
79 5.12.1
80
81 Authors
82 -------
83
84 * **Olivier Telle**
85 76
86 Acknowledgments 77 Acknowledgments
87 --------------- 78 ---------------
88 79
89 * Thomas Duigou 80 * Thomas Duigou
92 Licence 83 Licence
93 ------- 84 -------
94 85
95 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ 86 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
96 ]]></help> 87 ]]></help>
88 <creator>
89 <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" />
90 </creator>
97 </tool> 91 </tool>