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comparison tools/convert/SbmlWizard/SbmlWizard.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
comparison
equal deleted inserted replaced
9:0976a6257300 10:6a112eaf8f38
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="develop"> 2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.0">
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:develop</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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>
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65 <param name="inputPath" value="Human-GEM_pathways.xml"/> 59 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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72 <param name="removeIsolated" value="true"/> 60 <param name="removeIsolated" value="true"/>
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79 <param name="removeNoFlux" value="true"/> 61 <param name="removeNoFlux" value="true"/>
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86 <param name="mergingStrat" value="by_id"/> 62 <param name="mergingStrat" value="by_id"/>
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93 <param name="removeDuplicated" value="true"/> 63 <param name="removeDuplicated" value="true"/>
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100 <param name="exchangeCompToRemove" value="s"/> 64 <param name="exchangeCompToRemove" value="s"/>
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107 <output ftype="sbml" name="outputPath"> 65 <output ftype="sbml" name="outputPath">
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114 <assert_contents> 66 <assert_contents>
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121 <has_text text="&lt;/sbml&gt;"/> 67 <has_text text="&lt;/sbml&gt;"/>
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128 </assert_contents> 68 </assert_contents>
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135 </output> 69 </output>
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142 </test> 70 </test>
143 <test> 71 <test>
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150 <param name="inputPath" value="XF_network.sbml"/> 72 <param name="inputPath" value="XF_network.sbml"/>
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157 <param name="removeIsolated" value="true"/> 73 <param name="removeIsolated" value="true"/>
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164 <param name="removeNoFlux" value="true"/> 74 <param name="removeNoFlux" value="true"/>
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171 <param name="removeDuplicated" value="true"/> 75 <param name="removeDuplicated" value="true"/>
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178 <param name="inputSide" value="XF_network_C_Side.tab"/> 76 <param name="inputSide" value="XF_network_C_Side.tab"/>
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185 <param name="inputReactions" value="XF_network_R_Seed.tab"/> 77 <param name="inputReactions" value="XF_network_R_Seed.tab"/>
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192 <output ftype="sbml" name="outputPath"> 78 <output ftype="sbml" name="outputPath">
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199 <assert_contents> 79 <assert_contents>
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206 <has_text text="&lt;/sbml&gt;"/> 80 <has_text text="&lt;/sbml&gt;"/>
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213 </assert_contents> 81 </assert_contents>
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220 </output> 82 </output>
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227 </test> 83 </test>
228 </tests> 84 </tests>
229 <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> 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>
230 <citations/> 86 <citations/>
231 </tool> 87 </tool>