Mercurial > repos > tduigou > rpviz

comparison rpviz.xml @ 1:8057fdd27860 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:39:23 +0000
parents ea2ca40a24c5
children
comparison
equal deleted inserted replaced
0:ea2ca40a24c5 1:8057fdd27860
1 <tool id="rpviz" name="Visualize pathways" version="5.10.0"> 1 <tool id="rpviz" name="Visualize pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Visualize pathways from the RetroPath Suite</description> 2 <description>Visualize pathways from the RetroPath Suite</description>
3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">6.0.1</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="5.10.0">rptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
5 </requirements> 9 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
7 #set input_folder="input_folder" 11 #set input_folder="input_folder"
8 mkdir -p '$input_folder'; 12 mkdir -p '$input_folder' &&
9 #if str($input_type_conditional.input_type) == "sbml": 13 #if str($input_type_conditional.input_type) == "sbml":
10 #for $input in $input_type_conditional.input_sbml.keys(): 14 #for $input in $input_type_conditional.input_sbml.keys():
11 ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml'; 15 ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml' &&
12 #end for 16 #end for
13 python -m rptools.rpviz '$input_folder' 17 python -m rptools.rpviz '$input_folder'
14 #elif str($input_type_conditional.input_type) == "tar": 18 #elif str($input_type_conditional.input_type) == "tar":
15 python -m rptools.rpviz '${input_type_conditional.input_tar}' 19 python -m rptools.rpviz '${input_type_conditional.input_tar}'
16 #elif str($input_type_conditional.input_type) == "single_sbml": 20 #elif str($input_type_conditional.input_type) == "single_sbml":
17 ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}'; 21 ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}' &&
18 python -m rptools.rpviz '$input_folder' 22 python -m rptools.rpviz '$input_folder'
19 #end if 23 #end if
20 'out' 24 'out'
21 #if $adv.cofactor_file 25 #if $adv.cofactor_file
22 --cofactor '$adv.cofactor_file' 26 --cofactor '$adv.cofactor_file'
23 #end if 27 #end if
24 --autonomous_html '$html_file'; 28 --autonomous_html '$html_file' &&
25 rm -fr '$input_folder'; 29 rm -fr '$input_folder'
26 ]]></command> 30 ]]></command>
27 <inputs> 31 <inputs>
28 <conditional name="input_type_conditional"> 32 <conditional name="input_type_conditional">
29 <param name="input_type" type="select" label="Source SBML format"> 33 <param name="input_type" type="select" label="Source SBML format">
30 <option value="tar" selected="True">TAR</option> 34 <option value="tar" selected="True">TAR</option>
33 </param> 37 </param>
34 <when value="tar"> 38 <when value="tar">
35 <param name="input_tar" type="data" format="tar" label="Source SBML" /> 39 <param name="input_tar" type="data" format="tar" label="Source SBML" />
36 </when> 40 </when>
37 <when value="sbml"> 41 <when value="sbml">
38 <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> 42 <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" />
39 </when> 43 </when>
40 <when value="single_sbml"> 44 <when value="single_sbml">
41 <param name="input_single_sbml" type="data" format="xml" label="Source SBML" /> 45 <param name="input_single_sbml" type="data" format="sbml" label="Source SBML" />
42 </when> 46 </when>
43 </conditional> 47 </conditional>
44 <section name="adv" title="Advanced Options" expanded="false"> 48 <section name="adv" title="Advanced Options" expanded="false">
45 <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" /> 49 <param name="cofactor_file" type="data" format="tsv" optional="true" label="Cofactor file" help="File listing structures to consider as cofactors."/>
46 </section> 50 </section>
47 </inputs> 51 </inputs>
48 <outputs> 52 <outputs>
49 <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/> 53 <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
50 </outputs> 54 </outputs>
53 <!-- test 1: check if identical html output is produced (single sbml input) --> 57 <!-- test 1: check if identical html output is produced (single sbml input) -->
54 <conditional name="input_type_conditional"> 58 <conditional name="input_type_conditional">
55 <param name="input_type" value="single_sbml"/> 59 <param name="input_type" value="single_sbml"/>
56 <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" /> 60 <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
57 </conditional> 61 </conditional>
58 <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/> 62 <output name="html_file" >
63 <assert_contents>
64 <has_size value="1296252" delta="100" />
65 </assert_contents>
66 </output>
59 </test> 67 </test>
60 <test> 68 <test>
61 <!-- test 2: check if identical html output is produced (tar input) --> 69 <!-- test 2: check if identical html output is produced (tar input) -->
62 <conditional name="input_type_conditional"> 70 <conditional name="input_type_conditional">
63 <param name="input_type" value="tar"/> 71 <param name="input_type" value="tar"/>
64 <param name="input_tar" value="as_tar_inputs.tgz" /> 72 <param name="input_tar" value="as_tar_inputs.tgz" />
65 </conditional> 73 </conditional>
66 <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/> 74 <output name="html_file" >
75 <assert_contents>
76 <has_size value="1604488" delta="100" />
77 </assert_contents>
78 </output>
67 </test> 79 </test>
68 </tests> 80 </tests>
69 <help><![CDATA[ 81 <help><![CDATA[
70 RPVIZ 82 RPVIZ
71 ================ 83 ================
72 Visualize pathways from the RetroPath Suite 84
85 Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
73 86
74 Input 87 Input
75 ----- 88 -----
76 89
77 * **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder. 90 Required:
78 91
92 * **Source SBML**\ : Input file containing rpSBML files in a tar archive, collection or single file.
93
94 Optional:
95
96 * **Cofactor file**\ : File listing structures to consider as cofactors.
97
79 Output 98 Output
80 ------ 99 ------
81 100
82 * **output_folder**\ : (string) Output folder to be used. If it does not exist, an attempt will be made to create it.It the creation of the folder fails, IOError will be raised. 101 * **Pathways Visualization**\ : HTML output for pathway's visualization.
83 * **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies.
84 102
85 Project Links 103 Project Links
86 ------------------ 104 ------------------
87 105
88 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_ 106 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_
89
90 Version
91 ----------
92
93 5.10.0
94 107
95 License 108 License
96 ------- 109 -------
97 110
98 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ 111 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
99 112
100 ]]></help> 113 ]]></help>
114 <creator>
115 <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" />
116 </creator>
101 </tool> 117 </tool>