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comparison tools/attributes/GetEntities/GetEntities.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
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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_GetEntities" name="GetEntities" version="develop"> 2 <tool id="met4j_GetEntities" name="GetEntities" version="2.0.0">
3 <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</description> 3 <description>Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.</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 attributes.GetEntities -i "$sbml" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetEntities -i "$sbml"
11 $printMetabolites 11 $printMetabolites
12 $printReactions 12 $printReactions
13 $printCompartments 13 $printCompartments
28 <outputs> 28 <outputs>
29 <data format="tsv" name="outputFile"/> 29 <data format="tsv" name="outputFile"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
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39 <param name="sbml" value="Human-GEM_pathways.xml"/> 33 <param name="sbml" value="Human-GEM_pathways.xml"/>
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46 <output ftype="tsv" name="outputFile"> 34 <output ftype="tsv" name="outputFile">
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53 <assert_contents> 35 <assert_contents>
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60 <has_text_matching expression="GENE" n="86"/> 36 <has_text_matching expression="GENE" n="86"/>
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67 <has_text_matching expression="METABOLITE" n="111"/> 37 <has_text_matching expression="METABOLITE" n="111"/>
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74 <has_text_matching expression="REACTION" n="75"/> 38 <has_text_matching expression="REACTION" n="75"/>
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81 <has_text_matching expression="PATHWAY" n="3"/> 39 <has_text_matching expression="PATHWAY" n="3"/>
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88 <has_text_matching expression="COMPARTMENT" n="5"/> 40 <has_text_matching expression="COMPARTMENT" n="5"/>
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95 </assert_contents> 41 </assert_contents>
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102 </output> 42 </output>
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109 </test> 43 </test>
110 <test> 44 <test>
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117 <param name="sbml" value="Human-GEM_pathways.xml"/> 45 <param name="sbml" value="Human-GEM_pathways.xml"/>
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124 <param name="printReactions" value="true"/> 46 <param name="printReactions" value="true"/>
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131 <param name="printMetabolites" value="true"/> 47 <param name="printMetabolites" value="true"/>
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138 <param name="printGenes" value="true"/> 48 <param name="printGenes" value="true"/>
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145 <param name="printCompartments" value="true"/> 49 <param name="printCompartments" value="true"/>
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152 <param name="noTypeCol" value="true"/> 50 <param name="noTypeCol" value="true"/>
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159 <output ftype="tsv" name="outputFile"> 51 <output ftype="tsv" name="outputFile">
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166 <assert_contents> 52 <assert_contents>
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173 <has_n_lines n="277"/> 53 <has_n_lines n="277"/>
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180 </assert_contents> 54 </assert_contents>
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187 </output> 55 </output>
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194 </test> 56 </test>
195 </tests> 57 </tests>
196 <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help> 58 <help><![CDATA[Parse a SBML file to return a list of entities composing the network: metabolites, reactions, genes and others.The output file is a tabulated file with two columns, one with entity identifiers, and one with the entity type. If no entity type is selected, all of them are returned by default. Only identifiers are written, attributes can be extracted from dedicated apps or from the Sbml2Tab app.]]></help>
197 <citations/> 59 <citations/>
198 </tool> 60 </tool>