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Changeset 4:ae4c301919c4 (2022-11-17)

Previous changeset 3:6bd9aad9626d (2022-07-29) Next changeset 5:35c9abcd8934 (2023-01-12)

Commit message:
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5

diff -r 6bd9aad9626d -r ae4c301919c4 HowTo.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/HowTo.md Thu Nov 17 07:57:52 2022 +0000

[

@@ -0,0 +1,106 @@
+# How to build wrappers for new met4j-toolbox apps?
+
+## Install planemo
+
+```console
+virtualenv --python=/usr/bin/python3.8 .venv;
+source .venv/bin/activate
+pip install planemo
+```
+
+## Install singularity
+
+Doc [Here](https://github.com/sylabs/singularity/blob/main/INSTALL.md).
+
+## Create new wrappers
+
+1. Create a branch (e.g. newFeature) (or a new release) in met4j and develop your apps
+2. Push the branch
+3. If this branch is not master or develop, launch manually the
+building of the singularity image in the met4j CI-CD (this singularity image will be downloaded by the galaxy instance)
+4. Create a branch with the same name in met4j-galaxy (e.g. newFeature)
+5. Use the GenerateGalaxyFiles of the met4j-toolbox (be careful, it must be the version of the new branch) to generate the wrappers for the new met4j apps. Or you can use the singularity image created in the third step.
+
+```console
+met4j-toolbox.sif GenerateGalaxyFiles \
+ -o /path/to/met4j-galaxy/tools \
+ -v newFeature
+
+```
+
+Where newFeature is the name of the new branch.
+
+6. Edit manually the wrappers where the tests are lacking.
+
+[Here](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-tests) is the documentation about tests in galaxy
+
+Put the test files in a test-data directory in the tool directory.
+If the file is used in several tests, put it in the data directory at the root of the project and create a symbolic link in the test-data directory.
+
+7. Check the syntax of the wrappers
+
+```console
+source .venv/bin/activate
+planemo shed_lint --tools \
+--ensure_metadata \
+--urls \
+--report_level warn \
+--fail_level error \
+--recursive tools
+```
+
+8. Launch the tests
+
+Launching all the tests can be very time consuming.
+
+You can launch the test for one tool (here convert.Sbml2Graph):
+
+```console
+source .venv/bin/activate
+planemo test \
+--galaxy_source https://github.com/galaxyproject/galaxy \
+--galaxy_branch release_22.01 \
+--job_config_file config/job_conf.xml \
+tools/convert/Sbml2Graph/
+```
+
+or for an entire package (here convert):
+
+```console
+source .venv/bin/activate
+planemo test \
+--galaxy_source https://github.com/galaxyproject/galaxy \
+--galaxy_branch release_22.01 \
+--job_config_file config/job_conf.xml \
+tools/convert/Sbml2Graph/
+```
+
+If you want to test all the tools:
+
+```console
+source .venv/bin/activate
+planemo test \
+--galaxy_source https://github.com/galaxyproject/galaxy \
+--galaxy_branch release_22.01 \
+--job_config_file config/job_conf.xml
+```
+
+The results of the tests can be read in tool_test_output.html.
+
+9. If all the tests are ok, merge the new met4j branch in develop
+10. Create a new met4j release and finish the release: it will create a new singularity image for this version
+11. Launch once again GenerateGalaxyFiles
+
+```console
+met4j-toolbox.sif GenerateGalaxyFiles \
+ -o /path/to/met4j-galaxy/tools \
+ -v 1.1.1
+```
+
+where 1.1.1 is the number of the new release
+
+12. In met4j-galaxy, launch planemo lint to check if there is app without test and if everything is ok
+13. Test all the tools
+14. Merge on develop, create a new release, and push
+
+This will test again all the tools on the gitlab CI/CD. If it's ok, a new version of met4j-galaxy will be pushed on the galaxy toolshed. The instance in usegalaxy.fr will be updated the next monday.
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 README.rst
--- a/README.rst Fri Jul 29 13:23:40 2022 +0000
+++ b/README.rst Thu Nov 17 07:57:52 2022 +0000

[

@@ -4,6 +4,4 @@
Synopsis
--------

-This repository gathers tools built from [met4j-toolbox apps](https://forgemia.inra.fr/metexplore/met4j).
-
-![xml](https://link)
\ No newline at end of file
+This repository gathers tools built from [met4j-toolbox apps](https://forgemia.inra.fr/metexplore/met4j).
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/DecomposeSBML/DecomposeSBML.xml
--- a/tools/attributes/DecomposeSBML/DecomposeSBML.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/DecomposeSBML/DecomposeSBML.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_DecomposeSBML" name="DecomposeSBML" version="1.1.0">
+<tool id="met4j_DecomposeSBML" name="DecomposeSBML" version="1.2.0">
 <description>Parse SBML to render list of composing entities: metabolites, reactions, genes and others.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.DecomposeSBML -i "$sbml"
 $printMetabolites

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/ExtractPathways/ExtractPathways.xml
--- a/tools/attributes/ExtractPathways/ExtractPathways.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/ExtractPathways/ExtractPathways.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.1.0">
+<tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractPathways -i "$inputPath"
 -p "$pathwayId"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml
--- a/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="1.1.0">
+<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath"
 -export "$export"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml
--- a/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.1.0">
+<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.2.0">
 <description>Get gene lists from a list of reactions and a GSMN.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
 -r "$reactionFile"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml
--- a/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="1.1.0">
+<tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="1.2.0">
 <description>Get reactants lists from a list of reactions and a GSMN.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetReactantsFromReactions -i "$sbml"
 -r "$reactionFile"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml
--- a/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan':
 -cc "$colcharge"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml
--- a/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetEcsFromFile" name="SbmlSetEcsFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetEcsFromFile#if str($colec) != 'nan':
 -cec "$colec"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml
--- a/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetFormulasFromFile" name="SbmlSetFormulasFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetFormulasFromFile#if str($colformula) != 'nan':
 -cf "$colformula"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml
--- a/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetGprsFromFile" name="SbmlSetGprsFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetGprsFromFile#if str($colgpr) != 'nan':
 -cgpr "$colgpr"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_SbmlSetIdsFromFile" name="SbmlSetIdsFromFile" version="1.2.0">
+ <description>Set new ids to network objects from a tabulated file containing the old ids and the new ids</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetIdsFromFile#if str($colname) != 'nan':
+ -cnew "$colname"
+#end if
+#if str($colid):
+ -ci "$colid"
+#end if
+ $p
+ $s
+#if str($o):
+ -o "$o"
+#end if
+#if str($nSkip):
+ -n "$nSkip"
+#end if
+ -sbml "$sbml"
+#if str($tab) != 'None':
+ -tab "$tab"
+#end if
+#if str($c):
+ -c "$c"
+#end if
+ -out "$out"
+]]></command>
+ <inputs>
+ <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/>
+ <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
+ <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
+ <param argument="-o" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-sbml" format="sbml" label="Original sbml file" name="sbml" optional="false" type="data" value=""/>
+ <param argument="-tab" format="tsv" label="Tabulated file" name="tab" optional="true" type="data" value=""/>
+ <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ </inputs>
+ <outputs>
+ <data format="sbml" name="out"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="sbml" value="toy_model.xml"/>
+ <param name="tab" value="idMetabolites.tsv"/>
+ <param name="o" value="METABOLITE"/>
+ <output ftype="sbml" name="out">
+ <assert_contents>
+ <is_valid_xml/>
+ <has_line_matching expression=".*id=.metaboliteA.*" n="1"/>
+ <has_line_matching expression=".*id=.metaboliteB.*" n="1"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="toy_model.xml"/>
+ <param name="tab" value="idReactions.tsv"/>
+ <output ftype="sbml" name="out">
+ <assert_contents>
+ <is_valid_xml/>
+ <has_line_matching expression=".*id=.reaction1.*" n="1"/>
+ <has_line_matching expression=".*id=.reaction2.*" n="1"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="tab" value="idPathways.tsv"/>
+ <param name="o" value="PATHWAY"/>
+ <output ftype="sbml" name="out">
+ <assert_contents>
+ <is_valid_xml/>
+ <has_line_matching expression=".*groups:id=.CEB.*" n="1"/>
+ <has_line_matching expression=".*groups:id=.NSP.*" n="1"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="tab" value="idGenes.tsv"/>
+ <param name="o" value="GENE"/>
+ <output ftype="sbml" name="out">
+ <assert_contents>
+ <is_valid_xml/>
+ <has_line_matching expression=".*fbc:id=.G1.*" n="1"/>
+ <has_line_matching expression=".*fbc:id=.G2.*" n="1"/>
+ </assert_contents>
+ </output>
+ </test>
+ <test>
+ <param name="sbml" value="XF_network.sbml"/>
+ <param name="tab" value="idCompartments.tsv"/>
+ <param name="o" value="COMPARTMENT"/>
+ <output ftype="sbml" name="out">
+ <assert_contents>
+ <is_valid_xml/>
+ <has_line_matching expression=".*id=.cytosol.*" n="1"/>
+ <has_line_matching expression=".*id=.extra.*" n="1"/>
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
+ <help><![CDATA[Set new ids to network objects from a tabulated file containing the old ids and the new ids
+The ids must correspond between the tabulated file and the SBML file.
+If prefix or suffix is different in the SBML file, use the -p or the -s options.
+]]></help>
+ <citations/>
+</tool>

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/XF_network.sbml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/XF_network.sbml Thu Nov 17 07:57:52 2022 +0000

b'@@ -0,0 +1,47267 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<sbml fbc:required="false" groups:required="false" level="3" version="2" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">\n+ <model fbc:strict="true" id="Xfm1158" metaid="Xfm1158" name="Xfm1158">\n+ <fbc:listOfGeneProducts>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_007090" fbc:label="XFCFBP8418_007090" fbc:name="XFCFBP8418_007090" metaid="_8a7d7180-d79e-4dbb-86ed-f8d7eb60e698"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_005900" fbc:label="XFCFBP8418_005900" fbc:name="XFCFBP8418_005900" metaid="_867487dd-ff57-4e93-8de9-b5ecb805e0eb"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_011590" fbc:label="XFCFBP8418_011590" fbc:name="XFCFBP8418_011590" metaid="_44606760-936c-4585-b40c-650e953a5f73"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_014620" fbc:label="XFCFBP8418_014620" fbc:name="XFCFBP8418_014620" metaid="da273da9-0f84-4615-a464-2ab71416e8cc"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_015830" fbc:label="XFCFBP8418_015830" fbc:name="XFCFBP8418_015830" metaid="_3a9239a2-8e23-4834-99a8-a7dc15f6d906"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_014980" fbc:label="XFCFBP8418_014980" fbc:name="XFCFBP8418_014980" metaid="_7f26806b-e32e-4c5c-a78d-9e094c267bbf"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_020190" fbc:label="XFCFBP8418_020190" fbc:name="XFCFBP8418_020190" metaid="_31bbb514-1d52-4727-91cb-367af12e95ca"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_004940" fbc:label="XFCFBP8418_004940" fbc:name="XFCFBP8418_004940" metaid="a2f20753-c245-477e-8363-8f5e45c50f5d"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_021160" fbc:label="XFCFBP8418_021160" fbc:name="XFCFBP8418_021160" metaid="_844bdacc-d091-457d-9c4d-846cb9aab3c1"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_025760" fbc:label="XFCFBP8418_025760" fbc:name="XFCFBP8418_025760" metaid="fd8a601e-e56f-4263-9aa7-6ed9bf85f958"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_024670" fbc:label="XFCFBP8418_024670" fbc:name="XFCFBP8418_024670" metaid="_2bbe03ce-c814-417a-b9c0-e8a1f29f4106"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_004820" fbc:label="XFCFBP8418_004820" fbc:name="XFCFBP8418_004820" metaid="_41cb6d94-13d8-461e-a217-29a68e21cd2b"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_023580" fbc:label="XFCFBP8418_023580" fbc:name="XFCFBP8418_023580" metaid="_31ff72d7-4e30-4563-85aa-4afc58dd6bee"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_000460" fbc:label="XFCFBP8418_000460" fbc:name="XFCFBP8418_000460" metaid="d7ea14e6-cd6c-4404-b973-486ade662242"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_026730" fbc:label="XFCFBP8418_026730" fbc:name="XFCFBP8418_026730" metaid="e876348e-787e-4f2a-8904-e675c2589c17"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_025640" fbc:label="XFCFBP8418_025640" fbc:name="XFCFBP8418_025640" metaid="b5b93812-bd2e-4ca8-8328-e1d35e17ac3a"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_023100" fbc:label="XFCFBP8418_023100" fbc:name="XFCFBP8418_023100" metaid="f62e0096-7b12-4db3-a7b0-2e1cfa0302c6"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_027800" fbc:label="XFCFBP8418_027800" fbc:name="XFCFBP8418_027800" metaid="_8beb93ba-34a4-4330-86bf-2c47b1cb7f2e"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_004700" fbc:label="XFCFBP8418_004700" fbc:name="XFCFBP8418_004700" metaid="_2aceabe8-5294-42eb-9d3b-2506634c68d5"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_005910" fbc:label="XFCFBP8418_005910" fbc:name="XFCFBP8418_005910" metaid="a7b44241-024e-49c1-88af-1e1108cf09eb"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_013540" fbc:label="XFCFBP8418_013540" fbc:name="XFCFBP8418_013540" metaid="_83bdba7b-0eb0-4dfb-99ed-6e365240d870"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_011240" fbc:label="XFCFBP8418_011240" fbc:name="XFCFBP8418_011240" metaid="_568b9959-99b6-49bd-86d7-04e773d940da"/>\n+ <fbc:geneProduct fbc:id="XFCFBP8418_012210" fbc:label="XFCFBP8418_01221'..b' </annotation>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="XFCFBP8418_010590"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="M_cyst_L_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="M_2obut_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_cys_L_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_99999_0" fbc:upperFluxBound="UPPER_BOUND_99999_0" id="R_FUCtpp" metaid="_34363cfc-fa7f-4df4-a073-49f5befcdf50" name="R_FUCtpp" reversible="true">\n+ <notes>\n+ <body xmlns="http://www.w3.org/1999/xhtml">\n+ GENE_ASSOCIATION: XFCFBP8418_018650\n+ SUBSYSTEM: Transport__Inner_Membrane\n+ EC_NUMBER: No_Assignment\n+ </body>\n+ </notes>\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_34363cfc-fa7f-4df4-a073-49f5befcdf50">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/No_Assignment"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="XFCFBP8418_018650"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="M_h_p" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_fuc_L_p" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="M_fuc_L_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction fbc:lowerFluxBound="LOWER_BOUND_0_0" fbc:upperFluxBound="UPPER_BOUND_99999_0" id="R_FACOAE120" metaid="_2691931b-9cfe-40d9-95d9-13e4ed057413" name="R_FACOAE120" reversible="false">\n+ <notes>\n+ <body xmlns="http://www.w3.org/1999/xhtml">\n+ GENE_ASSOCIATION: XFCFBP8418_025070\n+ SUBSYSTEM: Cell_Envelope_Biosynthesis\n+ EC_NUMBER: 3.1.2.20\n+ </body>\n+ </notes>\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2691931b-9cfe-40d9-95d9-13e4ed057413">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.2.20"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="XFCFBP8418_025070"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_h_c" stoichiometry="1"/>\n+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ </listOfReactions>\n+ </model>\n+</sbml>\n'

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/idCompartments.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/idCompartments.tsv Thu Nov 17 07:57:52 2022 +0000

@@ -0,0 +1,2 @@
+c cytosol
+e extra
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/idGenes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/idGenes.tsv Thu Nov 17 07:57:52 2022 +0000

@@ -0,0 +1,2 @@
+XFCFBP8418_007090 G1
+XFCFBP8418_005900 G2
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/idMetabolites.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/idMetabolites.tsv Thu Nov 17 07:57:52 2022 +0000

@@ -0,0 +1,2 @@
+A metaboliteA
+B metaboliteB
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/idPathways.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/idPathways.tsv Thu Nov 17 07:57:52 2022 +0000

@@ -0,0 +1,2 @@
+Nucleotide_Salvage_Pathway NSP
+Cell_Envelope_Biosynthesis CEB
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/idReactions.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/idReactions.tsv Thu Nov 17 07:57:52 2022 +0000

@@ -0,0 +1,2 @@
+reac1 reaction1
+reac2 reaction2
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetIdsFromFile/test-data/toy_model.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/attributes/SbmlSetIdsFromFile/test-data/toy_model.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -0,0 +1,119 @@
+<?xml version="1.0" encoding='UTF-8' ?>
+<sbml fbc:required="false" groups:required="false" level="3" version="1"
+ xmlns="http://www.sbml.org/sbml/level3/version1/core"
+ xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"
+ xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1">
+ <model fbc:strict="true" name="toy model">
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
+ <listOfUnits>
+ <unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
+ <unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
+ <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment constant="false" id="c" name="Cytosol"/>
+ <compartment constant="false" id="e" name="Extracellular"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ SMILES: C[C@@H](C(=O)O)NC
+ </body>
+ </notes>
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#A_ext">
+ <bqbiol:is>
+ <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi>
+ </bqbiol:is>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+
+ </species>
+ <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/>
+ <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/>
+ <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/>
+ <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/>
+ <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/>
+ <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/>
+ <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/>
+ <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/>
+ <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/>
+ <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/>
+ <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/>
+ <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+ <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+ <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+ <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+ <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="A" stoichiometry="1.0"/>
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true">
+ <listOfReactants>
+ <speciesReference constant="true" species="A" stoichiometry="1.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="B" stoichiometry="1.0"/>
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" species="A" stoichiometry="1.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="C" stoichiometry="1.0"/>
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" species="B" stoichiometry="1.0"/>
+ <speciesReference constant="true" species="C" stoichiometry="1.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="D" stoichiometry="1.5"/>
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" species="D" stoichiometry="1.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/>
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="E" stoichiometry="1.0"/>
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false">
+ <listOfReactants>
+ <speciesReference constant="true" species="E" stoichiometry="2.0"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="D" stoichiometry="1.0"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
\ No newline at end of file

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml
--- a/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetNamesFromFile" name="SbmlSetNamesFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetNamesFromFile#if str($colname) != 'nan':
 -cname "$colname"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml
--- a/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetPathwaysFromFile" name="SbmlSetPathwaysFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetPathwaysFromFile#if str($colp) != 'nan':
 -cp "$colp"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml
--- a/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.1.0">
+<tool id="met4j_SbmlSetRefsFromFile" name="SbmlSetRefsFromFile" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlSetRefsFromFile#if str($colRef) != 'nan':
 -cr "$colRef"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml
--- a/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/attributes/SbmlToMetaboliteTable/SbmlToMetaboliteTable.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.1.0">
+<tool id="met4j_SbmlToMetaboliteTable" name="SbmlToMetaboliteTable" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SbmlToMetaboliteTable -s "$sbml"
 -o "$outputFile"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/bigg/GetModelProteome/GetModelProteome.xml
--- a/tools/bigg/GetModelProteome/GetModelProteome.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/bigg/GetModelProteome/GetModelProteome.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.1.0">
+<tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh bigg.GetModelProteome -m "$modelId"
 -o "$outputFile"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/convert/FbcToNotes/FbcToNotes.xml
--- a/tools/convert/FbcToNotes/FbcToNotes.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/convert/FbcToNotes/FbcToNotes.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_FbcToNotes" name="FbcToNotes" version="1.1.0">
+<tool id="met4j_FbcToNotes" name="FbcToNotes" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.FbcToNotes -i "$inputPath"
 -o "$outputPath"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/convert/Kegg2Sbml/Kegg2Sbml.xml
--- a/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/convert/Kegg2Sbml/Kegg2Sbml.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.1.0">
+<tool id="met4j_Kegg2Sbml" name="Kegg2Sbml" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Kegg2Sbml#if str($org):
 -org "$org"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/convert/Sbml2Graph/Sbml2Graph.xml
--- a/tools/convert/Sbml2Graph/Sbml2Graph.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/convert/Sbml2Graph/Sbml2Graph.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.1.0">
+<tool id="met4j_Sbml2Graph" name="Sbml2Graph" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Graph -i "$inputPath"
 $bipartite

diff -r 6bd9aad9626d -r ae4c301919c4 tools/convert/Sbml2Tab/Sbml2Tab.xml
--- a/tools/convert/Sbml2Tab/Sbml2Tab.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.1.0">
+<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i):
 -i "$i"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/convert/Tab2Sbml/Tab2Sbml.xml
--- a/tools/convert/Tab2Sbml/Tab2Sbml.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/convert/Tab2Sbml/Tab2Sbml.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.1.0">
+<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
 -ci "$colid"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/met4j.yml
--- a/tools/met4j.yml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/met4j.yml Thu Nov 17 07:57:52 2022 +0000

@@ -30,6 +30,9 @@
   - name: SbmlSetGprsFromFile
     owner: metexplore
     tool_panel_section_id: met4j_attributes
+  - name: SbmlSetIdsFromFile
+    owner: metexplore
+    tool_panel_section_id: met4j_attributes
   - name: SbmlSetNamesFromFile
     owner: metexplore
     tool_panel_section_id: met4j_attributes
@@ -63,12 +66,18 @@
   - name: CarbonSkeletonNet
     owner: metexplore
     tool_panel_section_id: met4j_networkanalysis
+  - name: ChemSimilarityWeighting
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
   - name: ChokePoint
     owner: metexplore
     tool_panel_section_id: met4j_networkanalysis
   - name: CompoundNet
     owner: metexplore
     tool_panel_section_id: met4j_networkanalysis
+  - name: DegreeWeighting
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
   - name: DistanceMatrix
     owner: metexplore
     tool_panel_section_id: met4j_networkanalysis
@@ -96,6 +105,9 @@
   - name: ScopeNetwork
     owner: metexplore
     tool_panel_section_id: met4j_networkanalysis
+  - name: SeedsAndTargets
+    owner: metexplore
+    tool_panel_section_id: met4j_networkanalysis
   - name: SideCompoundsScan
     owner: metexplore
     tool_panel_section_id: met4j_networkanalysis

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml
--- a/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.1.0">
+<tool id="met4j_CarbonSkeletonNet" name="CarbonSkeletonNet" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CarbonSkeletonNet -s "$inputPath"
 -g "$inputAAM"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_ChemSimilarityWeighting" name="ChemSimilarityWeighting" version="1.2.0">
+ <description>Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChemSimilarityWeighting#if str($type):
+ -f "$type"
+#end if
+#if str($smileFile):
+ -sm "$smileFile"
+#end if
+#if str($inchiFile):
+ -in "$inchiFile"
+#end if
+ $dist
+ -s "$inputPath"
+#if str($inputSide) != 'None':
+ -sc "$inputSide"
+#end if
+#if str($mergingStrat):
+ -mc "$mergingStrat"
+#end if
+ $mergeEdges
+ $undirected
+ $computeWeight
+ $removeNaN
+ -o "$outputPath"
+]]></command>
+ <inputs>
+ <param argument="-f" label="The chemical fingerprint to use" name="type" optional="true" type="select" value="Extended">
+ <option value="EState">EState</option>
+ <option selected="true" value="Extended">Extended</option>
+ <option value="KlekotaRoth">KlekotaRoth</option>
+ <option value="MACCS">MACCS</option>
+ <option value="PubChem">PubChem</option>
+ </param>
+ <param argument="-sm" label="If not present in SBML's annotations, get structure from a tabulated file with first column as compound id and second column as SMILE string, no header. Ignored if inchi file is provided" name="smileFile" optional="true" type="text" value="">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-in" label="If not present in SBML's annotations, get structure from a tabulated file with first column as compound id and second column as InChI string, no header." name="inchiFile" optional="true" type="text" value="">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-d" checked="false" falsevalue="" label="Use distance rather than similarity" name="dist" truevalue="-d" type="boolean" value="false"/>
+ <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+ <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
+ <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
+ <option selected="true" value="no">no</option>
+ <option value="by_name">by_name</option>
+ <option value="by_id">by_id</option>
+ </param>
+ <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
+ <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
+ <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
+ <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
+ </inputs>
+ <outputs>
+ <data format="" name="outputPath"/>
+ </outputs>
+ <tests/>
+ <help><![CDATA[Provides tabulated compound graph edge list, with one column with reactant pair's chemical similarity.Chemical similarity has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See McSha et al. 2003 (https://doi.org/10.1093/bioinformatics/btg217), Rahman et al. 2005 (https://doi.org/10.1093/bioinformatics/bti116) and Pertusi et al. 2014 (https://doi.org/10.1093/bioinformatics/btu760)]]></help>
+ <citations/>
+</tool>

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/ChokePoint/ChokePoint.xml
--- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ChokePoint" name="ChokePoint" version="1.1.0">
+<tool id="met4j_ChokePoint" name="ChokePoint" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/CompoundNet/CompoundNet.xml
--- a/tools/networkAnalysis/CompoundNet/CompoundNet.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/CompoundNet/CompoundNet.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_CompoundNet" name="CompoundNet" version="1.1.0">
+<tool id="met4j_CompoundNet" name="CompoundNet" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.CompoundNet -s "$inputPath"
#if str($inputSide) != 'None':

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/DegreeWeighting/DegreeWeighting.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_DegreeWeighting" name="DegreeWeighting" version="1.2.0">
+ <description>Provides tabulated compound graph edge list, with one column with target's degree.</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DegreeWeighting#if str($pow):
+ -pow "$pow"
+#end if
+ -s "$inputPath"
+#if str($inputSide) != 'None':
+ -sc "$inputSide"
+#end if
+#if str($mergingStrat):
+ -mc "$mergingStrat"
+#end if
+ $mergeEdges
+ $undirected
+ $computeWeight
+ $removeNaN
+ -o "$outputPath"
+]]></command>
+ <inputs>
+ <param argument="-pow" label="set weights as the degree raised to the power of number in parameter." name="pow" optional="true" type="text" value="1">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+ <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
+ <param argument="-mc" label="merge compartments. Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
+ <option selected="true" value="no">no</option>
+ <option value="by_name">by_name</option>
+ <option value="by_id">by_id</option>
+ </param>
+ <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
+ <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
+ <param argument="-tp" checked="false" falsevalue="" label="set weight as random walk transition probability, normalized by reaction" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
+ <param argument="-nan" checked="false" falsevalue="" label="do not output edges with undefined weight" name="removeNaN" truevalue="-nan" type="boolean" value="false"/>
+ </inputs>
+ <outputs>
+ <data format="" name="outputPath"/>
+ </outputs>
+ <tests/>
+ <help><![CDATA[Provides tabulated compound graph edge list, with one column with target's degree.Degree has been proposed as edge weight for finding meaningful paths in metabolic networks, using shortest (lightest) path search. See Croes et al. 2006 (https://doi.org/10.1016/j.jmb.2005.09.079) and Croes et al. 2005 (https://doi.org/10.1093/nar/gki437)]]></help>
+ <citations/>
+</tool>

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml
--- a/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.1.0">
+<tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="1.2.0">
 <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:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml
--- a/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.1.0">
+<tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.2.0">
 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
 -s "$sourcePath"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml
--- a/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.1.0">
+<tool id="met4j_ExtractSubNetwork" name="ExtractSubNetwork" version="1.2.0">
 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds of interests ids, one per row.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubNetwork -i "$inputPath"
 -s "$sourcePath"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml
--- a/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.1.0">
+<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="1.2.0">
 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/LoadPoint/LoadPoint.xml
--- a/tools/networkAnalysis/LoadPoint/LoadPoint.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/LoadPoint/LoadPoint.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_LoadPoint" name="LoadPoint" version="1.1.0">
+<tool id="met4j_LoadPoint" name="LoadPoint" version="1.2.0">
 <description>Compute the Load points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.LoadPoint -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/MetaboRank/MetaboRank.xml
--- a/tools/networkAnalysis/MetaboRank/MetaboRank.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/MetaboRank/MetaboRank.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_MetaboRank" name="MetaboRank" version="1.1.0">
+<tool id="met4j_MetaboRank" name="MetaboRank" version="1.2.0">
 <description>Compute the MetaboRank, a custom personalized PageRank for metabolic network.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.MetaboRank -i "$sbmlFilePath"
 -s "$seedsFilePath"

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/NetworkSummary/NetworkSummary.xml
--- a/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/NetworkSummary/NetworkSummary.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.1.0">
+<tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.2.0">
 <description>Create a report summarizing several graph measures characterising the structure of the network.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath"
#if str($sideCompoundFile) != 'None':

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml
--- a/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.1.0">
+<tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="1.2.0">
 <description>Perform a network expansion from a set of compound targets to create a precursor network.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath"
 -t "$targetsFilePath"
@@ -15,6 +15,7 @@
#if str($reactionToIgnoreFile) != 'None':
 -ir "$reactionToIgnoreFile"
#end if
+ $asTable
 -o "$output"
]]></command>
 <inputs>
@@ -22,6 +23,7 @@
 <param argument="-t" format="" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/>
 <param argument="-sc" format="" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/>
 <param argument="-ir" format="" label="an optional file containing list of reaction to ignore (forbid inclusion in scope)" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
+ <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
 </inputs>
 <outputs>
 <data format="gml" name="output"/>

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml
--- a/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.1.0">
+<tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.2.0">
 <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
 -s "$seedsFilePath"
@@ -17,6 +17,7 @@
 -ir "$reactionToIgnoreFile"
#end if
 $trace
+ $asTable
 -o "$output"
]]></command>
 <inputs>
@@ -26,6 +27,7 @@
 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/>
 <param argument="-ir" format="" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/>
+ <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
 </inputs>
 <outputs>
 <data format="gml" name="output"/>

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="1.2.0">
+ <description>Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology</description>
+ <xrefs>
+ <xref type="bio.tools">met4j</xref>
+ </xrefs>
+ <requirements>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
+ </requirements>
+ <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath"
+#if str($inputSide) != 'None':
+ -sc "$inputSide"
+#end if
+#if str($comp):
+ -c "$comp"
+#end if
+ $source
+ $sink
+ $notsource
+ $notsink
+ $keepIsolated
+ $useBorensteinAlg
+ $useInternal
+ -o "$outputPath"
+]]></command>
+ <inputs>
+ <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+ <param argument="-sc" format="" label="input Side compound file" name="inputSide" optional="true" type="data" value=""/>
+ <param argument="-c" label="Selected compartment(s), as model identifiers, separated by "+" sign if more than one" name="comp" optional="true" type="text" value="">
+ <sanitizer invalid_char="_">
+ <valid initial="string.printable"/>
+ </sanitizer>
+ </param>
+ <param argument="-s" checked="false" falsevalue="" label="export seeds" name="source" truevalue="-s" type="boolean" value="false"/>
+ <param argument="-t" checked="false" falsevalue="" label="export targets" name="sink" truevalue="-t" type="boolean" value="false"/>
+ <param argument="-!s" checked="false" falsevalue="" label="export nodes that are not seed" name="notsource" truevalue="-!s" type="boolean" value="false"/>
+ <param argument="-!t" checked="false" falsevalue="" label="export nodes that are not targets" name="notsink" truevalue="-!t" type="boolean" value="false"/>
+ <param argument="-is" checked="false" falsevalue="" label="do not ignore isolated nodes, consider isolated both seed and target" name="keepIsolated" truevalue="-is" type="boolean" value="false"/>
+ <param argument="-B" checked="false" falsevalue="" label="use Borenstein Algorithm. Please cite Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105). ignore internal option" name="useBorensteinAlg" truevalue="-B" type="boolean" value="false"/>
+ <param argument="-in" checked="false" falsevalue="" label="if an external compartment is defined, adjust degree by considering internal counterpart" name="useInternal" truevalue="-in" type="boolean" value="false"/>
+ </inputs>
+ <outputs>
+ <data format="" name="outputPath"/>
+ </outputs>
+ <tests/>
+ <help><![CDATA[Identify exogenously acquired compounds, producible compounds exogenously available and/or dead ends metabolites from metabolic network topology. Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms.
+This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment.
+The first method (see Borenstein et al. 2008 Large-scale reconstruction and phylogenetic analysis of metabolic environments https://doi.org/10.1073/pnas.0806162105) consider strongly connected components rather than individual nodes, thus, members of cycles can be considered as seed. A sink from an external compartment can however be connected to a non sink internal counterpart, thus highlighting what could end up in the external compartment rather than what must be exported.
+The second approach is neighborhood based and identify sources and sinks. Since "real" sinks and sources in intracellular compartment(s) may be involved in transport/exchange reactions reversible by default, thus not allowing extracellular source or sink, an option allows to take the degree (minus extracellular neighbors) of intracellular counterparts.]]></help>
+ <citations/>
+</tool>

diff -r 6bd9aad9626d -r ae4c301919c4 tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml
--- a/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml Thu Nov 17 07:57:52 2022 +0000

[

@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.1.0">
+<tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="1.2.0">
 <description>Scan a network to identify side-compounds.</description>
 <xrefs>
 <xref type="bio.tools">met4j</xref>
 </xrefs>
 <requirements>
- <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.1.0</container>
+ <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
 </requirements>
 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath"
 $sideOnly

diff -r 6bd9aad9626d -r ae4c301919c4 tools/tool_conf.xml
--- a/tools/tool_conf.xml Fri Jul 29 13:23:40 2022 +0000
+++ b/tools/tool_conf.xml Thu Nov 17 07:57:52 2022 +0000

@@ -11,6 +11,7 @@
 <tool file="met4j/attributes/SbmlSetEcsFromFile/SbmlSetEcsFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetFormulasFromFile/SbmlSetFormulasFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetGprsFromFile/SbmlSetGprsFromFile.xml"/>
+ <tool file="met4j/attributes/SbmlSetIdsFromFile/SbmlSetIdsFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetNamesFromFile/SbmlSetNamesFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetPathwaysFromFile/SbmlSetPathwaysFromFile.xml"/>
 <tool file="met4j/attributes/SbmlSetRefsFromFile/SbmlSetRefsFromFile.xml"/>
@@ -25,8 +26,10 @@
 <tool file="met4j/convert/Tab2Sbml/Tab2Sbml.xml"/>
 <section id="met4j_networkanalysis" name="Met4J - networkAnalysis"/>
 <tool file="met4j/networkAnalysis/CarbonSkeletonNet/CarbonSkeletonNet.xml"/>
+ <tool file="met4j/networkAnalysis/ChemSimilarityWeighting/ChemSimilarityWeighting.xml"/>
 <tool file="met4j/networkAnalysis/ChokePoint/ChokePoint.xml"/>
 <tool file="met4j/networkAnalysis/CompoundNet/CompoundNet.xml"/>
+ <tool file="met4j/networkAnalysis/DegreeWeighting/DegreeWeighting.xml"/>
 <tool file="met4j/networkAnalysis/DistanceMatrix/DistanceMatrix.xml"/>
 <tool file="met4j/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml"/>
 <tool file="met4j/networkAnalysis/ExtractSubNetwork/ExtractSubNetwork.xml"/>
@@ -36,5 +39,6 @@
 <tool file="met4j/networkAnalysis/NetworkSummary/NetworkSummary.xml"/>
 <tool file="met4j/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml"/>
 <tool file="met4j/networkAnalysis/ScopeNetwork/ScopeNetwork.xml"/>
+ <tool file="met4j/networkAnalysis/SeedsAndTargets/SeedsAndTargets.xml"/>
 <tool file="met4j/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml"/>
</toolbox>