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comparison tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml @ 11:40c15b7467f1 draft default tip

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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
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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_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.0"> 2 <tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="2.0.1">
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: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 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>
41
41 <param name="sbml" value="XF_network.sbml"/> 42 <param name="sbml" value="XF_network.sbml"/>
43
42 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 44 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
45
43 <output ftype="tsv" name="outputFile"> 46 <output ftype="tsv" name="outputFile">
47
44 <assert_contents> 48 <assert_contents>
49
45 <has_text_matching expression="R_GLUN" n="4"/> 50 <has_text_matching expression="R_GLUN" n="4"/>
51
46 <has_text_matching expression="R_ACGS" n="5"/> 52 <has_text_matching expression="R_ACGS" n="5"/>
53
47 </assert_contents> 54 </assert_contents>
55
48 </output> 56 </output>
57
49 </test> 58 </test>
50 <test> 59 <test>
60
51 <param name="sbml" value="XF_network.sbml"/> 61 <param name="sbml" value="XF_network.sbml"/>
62
52 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 63 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
64
53 <param name="printSubstrates" value="true"/> 65 <param name="printSubstrates" value="true"/>
66
54 <output ftype="tsv" name="outputFile"> 67 <output ftype="tsv" name="outputFile">
68
55 <assert_contents> 69 <assert_contents>
70
56 <has_text_matching expression="R_GLUN" n="2"/> 71 <has_text_matching expression="R_GLUN" n="2"/>
72
57 <has_text_matching expression="R_ACGS" n="5"/> 73 <has_text_matching expression="R_ACGS" n="5"/>
74
58 </assert_contents> 75 </assert_contents>
76
59 </output> 77 </output>
78
60 </test> 79 </test>
61 <test> 80 <test>
81
62 <param name="sbml" value="XF_network.sbml"/> 82 <param name="sbml" value="XF_network.sbml"/>
83
63 <param name="reactionFile" value="XF_network_R_Seed.tab"/> 84 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
85
64 <param name="printProducts" value="true"/> 86 <param name="printProducts" value="true"/>
87
65 <output ftype="tsv" name="outputFile"> 88 <output ftype="tsv" name="outputFile">
89
66 <assert_contents> 90 <assert_contents>
91
67 <has_text_matching expression="R_GLUN" n="2"/> 92 <has_text_matching expression="R_GLUN" n="2"/>
93
68 <has_text_matching expression="R_ACGS" n="5"/> 94 <has_text_matching expression="R_ACGS" n="5"/>
95
69 </assert_contents> 96 </assert_contents>
97
70 </output> 98 </output>
99
71 </test> 100 </test>
72 </tests> 101 </tests>
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> 102 <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/> 103 <citations/>
75 </tool> 104 </tool>