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comparison selenzy_wrapper.xml @ 1:9d092acc97ec draft default tip

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planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 0039ba858e95b91a07a018b2eece0e0737e6a20a
author tduigou
date Mon, 19 Jun 2023 11:22:39 +0000
parents ef4112ead31c
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0:ef4112ead31c 1:9d092acc97ec
1 <tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
2 <description>Performs enzyme selection from a reaction query</description> 2 <description>Performs enzyme selection from a reaction query</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">0.3.0</token> 5 <token name="@TOOL_VERSION@">0.3.0</token>
6 </macros> 6 </macros>
52 </outputs> 52 </outputs>
53 <tests> 53 <tests>
54 <test> 54 <test>
55 <!-- test 1: check if identical outputs are produced with default parameters --> 55 <!-- test 1: check if identical outputs are produced with default parameters -->
56 <param name="pathway" value="pathway.xml" /> 56 <param name="pathway" value="pathway.xml" />
57 <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/> 57 <output name="uniprot_ids">
58 <assert_contents>
59 <is_valid_xml />
60 <has_n_lines n="7968" />
61 </assert_contents>
62 </output>
58 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/> 63 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
59 </test> 64 </test>
60 <test> 65 <test>
61 <!-- test 2: check with taxon ID from a file --> 66 <!-- test 2: check with taxon ID from a file -->
62 <param name="pathway" value="pathway.xml" /> 67 <param name="pathway" value="pathway.xml" />
63 <conditional name="input_sim_type"> 68 <conditional name="input_sim_type">
64 <param name="host_taxID_type" value="tsv" /> 69 <param name="host_taxID_type" value="tsv" />
65 </conditional> 70 </conditional>
66 <param name="host_taxID_file" value="taxID.tsv" /> 71 <param name="host_taxID_file" value="taxID.tsv" />
67 <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/> 72 <output name="uniprot_ids">
73 <assert_contents>
74 <is_valid_xml />
75 <has_n_lines n="7968" />
76 </assert_contents>
77 </output>
68 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/> 78 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
69 </test> 79 </test>
70 </tests> 80 </tests>
71 <help><![CDATA[ 81 <help><![CDATA[
72 Selenzyme 82 Selenzyme
73 ================ 83 =========
74 84
75 Selenzyme searches for enzymes corresponding to each reaction of the pathway. It performs a reaction similarity search in the reference reaction database `MetaNetX <https://www.metanetx.org/>`_ and outputs an updated SBML file annotated with the enzyme UniProt IDs, as well as in CSV format. 85 Selenzyme searches for enzymes corresponding to each reaction of the pathway. It performs a reaction similarity search in the reference reaction database `MetaNetX <https://www.metanetx.org/>`_ and outputs an updated SBML file annotated with the enzyme UniProt IDs, as well as in CSV format.
76 86
77 Input 87 Input
78 ----- 88 -----
88 Output 98 Output
89 ------ 99 ------
90 100
91 * **Uniprot IDs (SBML)**\ : Annotated SBML pathway. 101 * **Uniprot IDs (SBML)**\ : Annotated SBML pathway.
92 * **Uniprot IDs (CSV)**\ : Annotated CSV pathway. 102 * **Uniprot IDs (CSV)**\ : Annotated CSV pathway.
93
94 Project Links
95 ------------------
96
97 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
98
99 Version
100 ----------
101
102 0.3.0
103
104 Authors
105 -------
106 * **Joan Hérisson**
107
108 License
109 -------
110
111 * `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
112
113 Acknowledgments
114 ---------------
115
116 * Thomas Duigou
117
118 ]]></help> 103 ]]></help>
104 <creator>
105 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
106 </creator>
119 <citations> 107 <citations>
120 <citation type="doi">10.1093/bioinformatics/bty065</citation> 108 <citation type="doi">10.1093/bioinformatics/bty065</citation>
121 </citations> 109 </citations>
122 </tool> 110 </tool>