Mercurial > repos > tduigou > rpreport
comparison rpreport.xml @ 1:3ea8aa1e94b4 draft default tip
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author | tduigou |
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date | Fri, 18 Nov 2022 16:32:44 +0000 |
parents | d09a51507aaf |
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0:d09a51507aaf | 1:3ea8aa1e94b4 |
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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> |