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comparison rpviz.xml @ 0:ea2ca40a24c5 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 17:40:42 +0000
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1 <tool id="rpviz" name="Visualize pathways" version="5.10.0">
2 <description>Visualize pathways from the RetroPath Suite</description>
3 <requirements>
4 <requirement type="package" version="5.10.0">rptools</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #set input_folder="input_folder"
8 mkdir -p '$input_folder';
9 #if str($input_type_conditional.input_type) == "sbml":
10 #for $input in $input_type_conditional.input_sbml.keys():
11 ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml';
12 #end for
13 python -m rptools.rpviz '$input_folder'
14 #elif str($input_type_conditional.input_type) == "tar":
15 python -m rptools.rpviz '${input_type_conditional.input_tar}'
16 #elif str($input_type_conditional.input_type) == "single_sbml":
17 ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}';
18 python -m rptools.rpviz '$input_folder'
19 #end if
20 'out'
21 #if $adv.cofactor_file
22 --cofactor '$adv.cofactor_file'
23 #end if
24 --autonomous_html '$html_file';
25 rm -fr '$input_folder';
26 ]]></command>
27 <inputs>
28 <conditional name="input_type_conditional">
29 <param name="input_type" type="select" label="Source SBML format">
30 <option value="tar" selected="True">TAR</option>
31 <option value="sbml">Collection</option>
32 <option value="single_sbml">single SBML</option>
33 </param>
34 <when value="tar">
35 <param name="input_tar" type="data" format="tar" label="Source SBML" />
36 </when>
37 <when value="sbml">
38 <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" />
39 </when>
40 <when value="single_sbml">
41 <param name="input_single_sbml" type="data" format="xml" label="Source SBML" />
42 </when>
43 </conditional>
44 <section name="adv" title="Advanced Options" expanded="false">
45 <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" />
46 </section>
47 </inputs>
48 <outputs>
49 <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
50 </outputs>
51 <tests>
52 <test>
53 <!-- test 1: check if identical html output is produced (single sbml input) -->
54 <conditional name="input_type_conditional">
55 <param name="input_type" value="single_sbml"/>
56 <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
57 </conditional>
58 <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/>
59 </test>
60 <test>
61 <!-- test 2: check if identical html output is produced (tar input) -->
62 <conditional name="input_type_conditional">
63 <param name="input_type" value="tar"/>
64 <param name="input_tar" value="as_tar_inputs.tgz" />
65 </conditional>
66 <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/>
67 </test>
68 </tests>
69 <help><![CDATA[
70 RPVIZ
71 ================
72 Visualize pathways from the RetroPath Suite
73
74 Input
75 -----
76
77 * **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder.
78
79 Output
80 ------
81
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.
83 * **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies.
84
85 Project Links
86 ------------------
87
88 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_
89
90 Version
91 ----------
92
93 5.10.0
94
95 License
96 -------
97
98 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
99
100 ]]></help>
101 </tool>