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comparison tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.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
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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_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop"> 2 <tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.0">
3 <description>Get reactant lists from a list of reactions and a SBML file.</description> 3 <description>Get reactant lists from a list of reactions and a SBML file.</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.GetReactantsFromReactions -i "$sbml" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml"
11 -r "$reactionFile" 11 -r "$reactionFile"
12 #if str($sep): 12 #if str($sep):
13 -sep "$sep" 13 -sep "$sep"
36 <outputs> 36 <outputs>
37 <data format="tsv" name="outputFile"/> 37 <data format="tsv" name="outputFile"/>
38 </outputs> 38 </outputs>
39 <tests> 39 <tests>
40 <test> 40 <test>
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52 <param name="sbml" value="XF_network.sbml"/> 41 <param name="sbml" value="XF_network.sbml"/>
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64 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 42 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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76 <output ftype="tsv" name="outputFile"> 43 <output ftype="tsv" name="outputFile">
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88 <assert_contents> 44 <assert_contents>
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100 <has_text_matching expression="R_GLUN" n="4"/> 45 <has_text_matching expression="R_GLUN" n="4"/>
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112 <has_text_matching expression="R_ACGS" n="5"/> 46 <has_text_matching expression="R_ACGS" n="5"/>
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124 </assert_contents> 47 </assert_contents>
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136 </output> 48 </output>
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148 </test> 49 </test>
149 <test> 50 <test>
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161 <param name="sbml" value="XF_network.sbml"/> 51 <param name="sbml" value="XF_network.sbml"/>
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173 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 52 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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185 <param name="printSubstrates" value="true"/> 53 <param name="printSubstrates" value="true"/>
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197 <output ftype="tsv" name="outputFile"> 54 <output ftype="tsv" name="outputFile">
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209 <assert_contents> 55 <assert_contents>
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221 <has_text_matching expression="R_GLUN" n="2"/> 56 <has_text_matching expression="R_GLUN" n="2"/>
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233 <has_text_matching expression="R_ACGS" n="5"/> 57 <has_text_matching expression="R_ACGS" n="5"/>
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245 </assert_contents> 58 </assert_contents>
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257 </output> 59 </output>
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269 </test> 60 </test>
270 <test> 61 <test>
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282 <param name="sbml" value="XF_network.sbml"/> 62 <param name="sbml" value="XF_network.sbml"/>
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294 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 63 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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306 <param name="printProducts" value="true"/> 64 <param name="printProducts" value="true"/>
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318 <output ftype="tsv" name="outputFile"> 65 <output ftype="tsv" name="outputFile">
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330 <assert_contents> 66 <assert_contents>
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342 <has_text_matching expression="R_GLUN" n="2"/> 67 <has_text_matching expression="R_GLUN" n="2"/>
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354 <has_text_matching expression="R_ACGS" n="5"/> 68 <has_text_matching expression="R_ACGS" n="5"/>
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366 </assert_contents> 69 </assert_contents>
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378 </output> 70 </output>
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390 </test> 71 </test>
391 </tests> 72 </tests>
392 <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help> 73 <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>
393 <citations/> 74 <citations/>
394 </tool> 75 </tool>