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comparison tools/convert/SbmlWizard/SbmlWizard.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
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children 6a112eaf8f38
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="develop">
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:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath"
11 #if str($inputSide) != 'None':
12 -rc "$inputSide"
13 #end if
14 #if str($toKeepC) != 'None':
15 -kc "$toKeepC"
16 #end if
17 $removeIsolated
18 #if str($inputReactions) != 'None':
19 -rr "$inputReactions"
20 #end if
21 #if str($toKeepR) != 'None':
22 -kr "$toKeepR"
23 #end if
24 $removeNoFlux
25 #if str($mergingStrat):
26 -mc "$mergingStrat"
27 #end if
28 $removeDuplicated
29 #if str($exchangeCompToRemove):
30 -rEX "$exchangeCompToRemove"
31 #end if
32 -o "$outputPath"
33 ]]></command>
34 <inputs>
35 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
36 <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/>
37 <param argument="-kc" format="txt" label="file containing identifiers of compounds to keep from the metabolic network" name="toKeepC" optional="true" type="data" value=""/>
38 <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/>
39 <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/>
40 <param argument="-kr" format="txt" label="file containing identifiers of reactions to keep from the metabolic network" name="toKeepR" optional="true" type="data" value=""/>
41 <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"/>
42 <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">
43 <option selected="true" value="no">no</option>
44 <option value="by_name">by_name</option>
45 <option value="by_id">by_id</option>
46 </param>
47 <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/>
48 <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value="">
49 <sanitizer invalid_char="_">
50 <valid initial="string.printable"/>
51 </sanitizer>
52 </param>
53 </inputs>
54 <outputs>
55 <data format="sbml" name="outputPath"/>
56 </outputs>
57 <tests>
58 <test>
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65 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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72 <param name="removeIsolated" value="true"/>
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79 <param name="removeNoFlux" value="true"/>
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86 <param name="mergingStrat" value="by_id"/>
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93 <param name="removeDuplicated" value="true"/>
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100 <param name="exchangeCompToRemove" value="s"/>
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107 <output ftype="sbml" name="outputPath">
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114 <assert_contents>
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121 <has_text text="&lt;/sbml&gt;"/>
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128 </assert_contents>
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135 </output>
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142 </test>
143 <test>
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150 <param name="inputPath" value="XF_network.sbml"/>
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157 <param name="removeIsolated" value="true"/>
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164 <param name="removeNoFlux" value="true"/>
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171 <param name="removeDuplicated" value="true"/>
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178 <param name="inputSide" value="XF_network_C_Side.tab"/>
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185 <param name="inputReactions" value="XF_network_R_Seed.tab"/>
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192 <output ftype="sbml" name="outputPath">
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199 <assert_contents>
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206 <has_text text="&lt;/sbml&gt;"/>
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213 </assert_contents>
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220 </output>
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227 </test>
228 </tests>
229 <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>
230 <citations/>
231 </tool>