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Commit 12798951 authored by lcottret's avatar lcottret
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Finish 0.12.0

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<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ExtractPathways" name="ExtractPathways" version="0.11.0">
<tool id="met4j_ExtractPathways" name="ExtractPathways" version="0.12.0">
<description>Extract pathway(s) from GSMN</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath"
-p "$pathwayId"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="0.11.0">
<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="0.12.0">
<description>Extract databases' references from SBML annotations or notes.</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath"
-export "$export"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.11.0">
<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="0.12.0">
<description>Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
-cc "$colcharge"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.11.0">
<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="0.12.0">
<description>Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan':
-cec "$colec"
......@@ -66,7 +66,7 @@
<help><![CDATA[Set EC numbers to reactions from a tabulated file containing the reaction ids and the EC
The ids must correspond between the tabulated file and the SBML file.
If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
The EC will be written in the SBML file in two locations:+
The EC will be written in the SBML file in two locations:
- in the reaction notes (e.g. <p>EC_NUMBER: 2.4.2.14</p>)
- as a reaction annotation (e.g. <rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.2.14"/>)]]></help>
<citations/>
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.11.0">
<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="0.12.0">
<description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
-cf "$colformula"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.11.0">
<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="0.12.0">
<description>Create a new SBML file from an original sbml file and a tabulated file containing reaction ids and Gene association written in a cobra way</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
-cgpr "$colgpr"
......@@ -72,12 +72,12 @@ If prefix R_ is present in the ids in the SBML file and not in the tabulated fil
GPR must be written in a cobra way in the tabulated file as described in Schellenberger et al 2011 Nature Protocols 6(9):1290-307
(The GPR will be written in the SBML file in two locations:
- in the reaction notes <p>GENE_ASSOCIATION: ( XC_0401 ) OR ( XC_3282 )</p>
- as fbc gene product association : <fbc:geneProductAssociation>
<fbc:or>
<fbc:geneProductRef fbc:geneProduct="XC_3282"/>
<fbc:geneProductRef fbc:geneProduct="XC_0401"/>
</fbc:or>
</fbc:geneProductAssociation>
- as fbc gene product association :<fbc:geneProductAssociation>
<fbc:or>
<fbc:geneProductRef fbc:geneProduct="XC_3282"/>
<fbc:geneProductRef fbc:geneProduct="XC_0401"/>
</fbc:or>
</fbc:geneProductAssociation>
]]></help>
<citations/>
</tool>
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="0.11.0">
<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="0.12.0">
<description>Set names to network objects from a tabulated file containing the object ids and the names</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan':
-cname "$colname"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.11.0">
<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="0.12.0">
<description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
-cp "$colp"
......@@ -87,10 +87,10 @@
The ids must correspond between the tabulated file and the SBML file.
If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
Pathways will be written in the SBML file in two ways:- as reaction note (e.g. <p>SUBSYSTEM: purine_biosynthesis</p>)- as SBML group:
<groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
<groups:listOfMembers>
<groups:member groups:idRef="R_GLUPRT"/>
<groups:member groups:idRef="R_RNDR1b"/>
<groups:group groups:id="purine_biosynthesis" groups:kind="classification" groups:name="purine_biosynthesis">
<groups:listOfMembers>
<groups:member groups:idRef="R_GLUPRT"/>
<groups:member groups:idRef="R_RNDR1b"/>
...
]]></help>
<citations/>
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="0.11.0">
<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="0.12.0">
<description>Add refs to network objects from a tabulated file containing the metabolite ids and the formulas</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
-cr "$colRef"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="0.11.0">
<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="0.12.0">
<description>Create a tabulated file with metabolite attributes from a SBML file</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml"
-o "$outputFile"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_GetModelProteome" name="GetModelProteome" version="0.11.0">
<tool id="met4j_GetModelProteome" name="GetModelProteome" version="0.12.0">
<description>Get proteome in fasta format of a model present in BIGG</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId"
-o "$outputFile"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_FbcToNotes" name="FbcToNotes" version="0.11.0">
<tool id="met4j_FbcToNotes" name="FbcToNotes" version="0.12.0">
<description>Convert FBC package annotations to sbml notes</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath"
-o "$outputPath"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.11.0">
<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="0.12.0">
<description>Build a SBML file from KEGG organism-specific pathways. Uses Kegg API.</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org):
-org "$org"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.11.0">
<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="0.12.0">
<description>Create a graph representation of a SBML file content, and export it in graph file format.</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
$bipartite
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="0.11.0">
<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="0.12.0">
<description>Create a tabulated file from a SBML file</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
-i "$i"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="0.11.0">
<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="0.12.0">
<description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
-ci "$colid"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.11.0">
<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="0.12.0">
<description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
-g "$inputAAM"
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ChokePoint" name="ChokePoint" version="0.11.0">
<tool id="met4j_ChokePoint" name="ChokePoint" version="0.12.0">
<description>Compute the Choke points of a metabolic network.</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
#if str($sideCompoundFile) != 'None':
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_CompoundNet" name="CompoundNet" version="0.11.0">
<tool id="met4j_CompoundNet" name="CompoundNet" version="0.12.0">
<description>Advanced creation of a compound graph representation of a SBML file content</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
#if str($inputSide) != 'None':
......
<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.11.0">
<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="0.12.0">
<description>Create a compound to compound distance matrix.</description>
<xrefs>
<xref type="bio.tools">met4j</xref>
</xrefs>
<requirements>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container>
<container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
#if str($sideCompoundFile) != 'None':
......
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