Mercurial > repos > metexplore > met4j

comparison build/tools/SbmlWizard/SbmlWizard.xml @ 11:40c15b7467f1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
comparison
equal deleted inserted replaced
10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.0"> 2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.1">
3 <description>General SBML model processing</description> 3 <description>General SBML model processing</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath"
11 #if str($inputSide) != 'None': 11 #if str($inputSide) != 'None':
12 -rc "$inputSide" 12 -rc "$inputSide"
13 #end if 13 #end if
54 <outputs> 54 <outputs>
55 <data format="sbml" name="outputPath"/> 55 <data format="sbml" name="outputPath"/>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <test> 58 <test>
59
59 <param name="inputPath" value="Human-GEM_pathways.xml"/> 60 <param name="inputPath" value="Human-GEM_pathways.xml"/>
61
60 <param name="removeIsolated" value="true"/> 62 <param name="removeIsolated" value="true"/>
63
61 <param name="removeNoFlux" value="true"/> 64 <param name="removeNoFlux" value="true"/>
65
62 <param name="mergingStrat" value="by_id"/> 66 <param name="mergingStrat" value="by_id"/>
67
63 <param name="removeDuplicated" value="true"/> 68 <param name="removeDuplicated" value="true"/>
69
64 <param name="exchangeCompToRemove" value="s"/> 70 <param name="exchangeCompToRemove" value="s"/>
71
65 <output ftype="sbml" name="outputPath"> 72 <output ftype="sbml" name="outputPath">
73
66 <assert_contents> 74 <assert_contents>
75
67 <has_text text="&lt;/sbml&gt;"/> 76 <has_text text="&lt;/sbml&gt;"/>
77
68 </assert_contents> 78 </assert_contents>
79
69 </output> 80 </output>
81
70 </test> 82 </test>
71 <test> 83 <test>
84
72 <param name="inputPath" value="XF_network.sbml"/> 85 <param name="inputPath" value="XF_network.sbml"/>
86
73 <param name="removeIsolated" value="true"/> 87 <param name="removeIsolated" value="true"/>
88
74 <param name="removeNoFlux" value="true"/> 89 <param name="removeNoFlux" value="true"/>
90
75 <param name="removeDuplicated" value="true"/> 91 <param name="removeDuplicated" value="true"/>
92
76 <param name="inputSide" value="XF_network_C_Side.tab"/> 93 <param name="inputSide" value="XF_network_C_Side.tab"/>
94
77 <param name="inputReactions" value="XF_network_R_Seed.tab"/> 95 <param name="inputReactions" value="XF_network_R_Seed.tab"/>
96
78 <output ftype="sbml" name="outputPath"> 97 <output ftype="sbml" name="outputPath">
98
79 <assert_contents> 99 <assert_contents>
100
80 <has_text text="&lt;/sbml&gt;"/> 101 <has_text text="&lt;/sbml&gt;"/>
102
81 </assert_contents> 103 </assert_contents>
104
82 </output> 105 </output>
106
83 </test> 107 </test>
84 </tests> 108 </tests>
85 <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help> 109 <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help>
86 <citations/> 110 <citations/>
87 </tool> 111 </tool>