Mercurial > repos > metexplore > met4j

annotate build/tools/SbmlWizard/SbmlWizard.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
children
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.1">
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3 <description>General SBML model processing</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath"
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11 #if str($inputSide) != 'None':
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12 -rc "$inputSide"
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13 #end if
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14 #if str($toKeepC) != 'None':
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15 -kc "$toKeepC"
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16 #end if
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17 $removeIsolated
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18 #if str($inputReactions) != 'None':
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19 -rr "$inputReactions"
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20 #end if
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21 #if str($toKeepR) != 'None':
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22 -kr "$toKeepR"
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23 #end if
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24 $removeNoFlux
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25 #if str($mergingStrat):
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26 -mc "$mergingStrat"
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27 #end if
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28 $removeDuplicated
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29 #if str($exchangeCompToRemove):
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30 -rEX "$exchangeCompToRemove"
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31 #end if
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32 -o "$outputPath"
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33 ]]></command>
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34 <inputs>
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35 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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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=""/>
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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=""/>
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38 <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/>
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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=""/>
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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=""/>
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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"/>
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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">
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43 <option selected="true" value="no">no</option>
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44 <option value="by_name">by_name</option>
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45 <option value="by_id">by_id</option>
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46 </param>
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47 <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/>
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48 <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value="">
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49 <sanitizer invalid_char="_">
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50 <valid initial="string.printable"/>
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51 </sanitizer>
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52 </param>
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53 </inputs>
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54 <outputs>
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55 <data format="sbml" name="outputPath"/>
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56 </outputs>
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57 <tests>
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58 <test>
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60 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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62 <param name="removeIsolated" value="true"/>
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64 <param name="removeNoFlux" value="true"/>
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65
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66 <param name="mergingStrat" value="by_id"/>
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68 <param name="removeDuplicated" value="true"/>
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70 <param name="exchangeCompToRemove" value="s"/>
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72 <output ftype="sbml" name="outputPath">
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74 <assert_contents>
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76 <has_text text="&lt;/sbml&gt;"/>
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78 </assert_contents>
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80 </output>
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82 </test>
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83 <test>
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85 <param name="inputPath" value="XF_network.sbml"/>
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87 <param name="removeIsolated" value="true"/>
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89 <param name="removeNoFlux" value="true"/>
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91 <param name="removeDuplicated" value="true"/>
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93 <param name="inputSide" value="XF_network_C_Side.tab"/>
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94
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95 <param name="inputReactions" value="XF_network_R_Seed.tab"/>
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96
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97 <output ftype="sbml" name="outputPath">
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98
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99 <assert_contents>
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100
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101 <has_text text="&lt;/sbml&gt;"/>
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102
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103 </assert_contents>
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104
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105 </output>
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106
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107 </test>
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108 </tests>
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109 <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>
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110 <citations/>
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111 </tool>