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comparison tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 7a6f2380fc1d
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop">
3 <description>Get reactants lists from a list of reactions and a GSMN.</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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</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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41 <param name="sbml" value="XF_network.sbml"/> 52 <param name="sbml" value="XF_network.sbml"/>
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42 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 64 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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43 <output ftype="tsv" name="outputFile"> 76 <output ftype="tsv" name="outputFile">
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44 <assert_contents> 88 <assert_contents>
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45 <has_text_matching expression="R_GLUN" n="4"/> 100 <has_text_matching expression="R_GLUN" n="4"/>
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46 <has_text_matching expression="R_ACGS" n="5"/> 112 <has_text_matching expression="R_ACGS" n="5"/>
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47 </assert_contents> 124 </assert_contents>
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48 </output> 136 </output>
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49 </test> 148 </test>
50 <test> 149 <test>
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51 <param name="sbml" value="XF_network.sbml"/> 161 <param name="sbml" value="XF_network.sbml"/>
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52 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 173 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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53 <param name="printSubstrates" value="true"/> 185 <param name="printSubstrates" value="true"/>
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54 <output ftype="tsv" name="outputFile"> 197 <output ftype="tsv" name="outputFile">
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55 <assert_contents> 209 <assert_contents>
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56 <has_text_matching expression="R_GLUN" n="2"/> 221 <has_text_matching expression="R_GLUN" n="2"/>
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57 <has_text_matching expression="R_ACGS" n="5"/> 233 <has_text_matching expression="R_ACGS" n="5"/>
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58 </assert_contents> 245 </assert_contents>
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59 </output> 257 </output>
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60 </test> 269 </test>
61 <test> 270 <test>
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62 <param name="sbml" value="XF_network.sbml"/> 282 <param name="sbml" value="XF_network.sbml"/>
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63 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 294 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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64 <param name="printProducts" value="true"/> 306 <param name="printProducts" value="true"/>
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65 <output ftype="tsv" name="outputFile"> 318 <output ftype="tsv" name="outputFile">
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66 <assert_contents> 330 <assert_contents>
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67 <has_text_matching expression="R_GLUN" n="2"/> 342 <has_text_matching expression="R_GLUN" n="2"/>
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68 <has_text_matching expression="R_ACGS" n="5"/> 354 <has_text_matching expression="R_ACGS" n="5"/>
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69 </assert_contents> 366 </assert_contents>
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70 </output> 378 </output>
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71 </test> 390 </test>
72 </tests> 391 </tests>
73 <help><![CDATA[Get reactants lists from a list of reactions and a GSMN. 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 both substrates and products]]></help> 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>
74 <citations/> 393 <citations/>
75 </tool> 394 </tool>