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comparison tools/convert/SBMLwizard/SBMLwizard.xml @ 7:1436e9cde9c9 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
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6:7a6f2380fc1d 7:1436e9cde9c9
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_SBMLwizard" name="SBMLwizard" version="MET4J_VERSION_TEST">
3 <description>General SBML model processing</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$inputPath"
11 #if str($inputSide) != 'None':
12 -rc "$inputSide"
13 #end if
14 $removeIsolated
15 #if str($inputReactions) != 'None':
16 -rr "$inputReactions"
17 #end if
18 $removeNoFlux
19 #if str($mergingStrat):
20 -mc "$mergingStrat"
21 #end if
22 $removeDuplicated
23 #if str($exchangeCompToRemove):
24 -rEX "$exchangeCompToRemove"
25 #end if
26 -o "$outputPath"
27 ]]></command>
28 <inputs>
29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
30 <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/>
31 <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/>
32 <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/>
33 <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/>
34 <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. &quot;by_name&quot; can be used if names are consistent and unambiguous across compartments, &quot;by_id&quot; can be used if compartment suffix is present in compounds identifiers (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
35 <option selected="true" value="no">no</option>
36 <option value="by_name">by_name</option>
37 <option value="by_id">by_id</option>
38 </param>
39 <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/>
40 <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value="">
41 <sanitizer invalid_char="_">
42 <valid initial="string.printable"/>
43 </sanitizer>
44 </param>
45 </inputs>
46 <outputs>
47 <data format="sbml" name="outputPath"/>
48 </outputs>
49 <tests>
50 <test>
51 <param name="inputPath" value="Human-GEM_pathways.xml"/>
52 <param name="removeIsolated" value="true"/>
53 <param name="removeNoFlux" value="true"/>
54 <param name="mergingStrat" value="by_id"/>
55 <param name="removeDuplicated" value="true"/>
56 <param name="exchangeCompToRemove" value="s"/>
57 <output ftype="sbml" name="outputPath">
58 <assert_contents>
59 <has_text text="&lt;/sbml&gt;"/>
60 </assert_contents>
61 </output>
62 </test>
63 <test>
64 <param name="inputPath" value="XF_network.sbml"/>
65 <param name="removeIsolated" value="true"/>
66 <param name="removeNoFlux" value="true"/>
67 <param name="removeDuplicated" value="true"/>
68 <param name="inputSide" value="XF_network_C_Side.tab"/>
69 <param name="inputReactions" value="XF_network_R_Seed.tab"/>
70 <output ftype="sbml" name="outputPath">
71 <assert_contents>
72 <has_text text="&lt;/sbml&gt;"/>
73 </assert_contents>
74 </output>
75 </test>
76 </tests>
77 <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>
78 <citations/>
79 </tool>