Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/SideCompoundsScan/SideCompoundsScan.xml @ 1:9b162ee6ff8e draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
| author | metexplore |
|---|---|
| date | Mon, 27 Jun 2022 13:41:08 +0000 |
| parents | dcd16521b969 |
| children | e69a78624877 |
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| 0:dcd16521b969 | 1:9b162ee6ff8e |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="0.11.0"> | 2 <tool id="met4j_SideCompoundsScan" name="SideCompoundsScan" version="0.12.0"> |
| 3 <description>Scan a network to identify side-compounds.</description> | 3 <description>Scan a network to identify side-compounds.</description> |
| 4 <xrefs> | 4 <xrefs> |
| 5 <xref type="bio.tools">met4j</xref> | 5 <xref type="bio.tools">met4j</xref> |
| 6 </xrefs> | 6 </xrefs> |
| 7 <requirements> | 7 <requirements> |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.11.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container> |
| 9 </requirements> | 9 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SideCompoundsScan -i "$inputPath" |
| 11 $sideOnly | 11 $sideOnly |
| 12 $noReportValue | 12 $noReportValue |
| 13 #if str($degree): | 13 #if str($degree): |
| 78 - *Neighbor Coupling*: Similar to degree, this criteria assume that side compounds are involved in many reactions, but in pairs with other side compounds. | 78 - *Neighbor Coupling*: Similar to degree, this criteria assume that side compounds are involved in many reactions, but in pairs with other side compounds. |
| 79 Therefore, the transition from ATP to ADP will appear multiple time in the network, creating redundant 'parallel edges' between these two neighbors. | 79 Therefore, the transition from ATP to ADP will appear multiple time in the network, creating redundant 'parallel edges' between these two neighbors. |
| 80 Being tightly coupled to another compound through a high number of redundant edges, can point out cofactors while keeping converging pathways' products with high degree like pyruvate aside. | 80 Being tightly coupled to another compound through a high number of redundant edges, can point out cofactors while keeping converging pathways' products with high degree like pyruvate aside. |
| 81 - *Carbon Count*: Metabolic "waste", or degradation end-product such as ammonia or carbon dioxide are usually considered as side compounds. | 81 - *Carbon Count*: Metabolic "waste", or degradation end-product such as ammonia or carbon dioxide are usually considered as side compounds. |
| 82 Most of them are inorganic compound, another ill-defined concept, sometimes defined as compound lacking C-C or C-H bonds. Since chemical structure is rarely available in SBML model beyond chemical formula, we use a less restrictive criterion by flagging compound with one or no carbons. This cover most inorganic compounds, but include few compounds such as methane usually considered as organic. - *Chemical Formula*: Metabolic network often contains 'artifacts' that serve modelling purpose (to define a composite objective function for example). Such entities can be considered as 'side entities'. Since they are not actual chemical compounds, they can be detected by their lack of valid chemical formula. However, this can also flag main compounds with erroneous or missing annotation.]]></help> | 82 Most of them are inorganic compound, another ill-defined concept, sometimes defined as compound lacking C-C or C-H bonds. Since chemical structure is rarely available in SBML model beyond chemical formula, we use a less restrictive criterion by flagging compound with one or no carbons. This cover most inorganic compounds, but include few compounds such as methane usually considered as organic. - *Chemical Formula*: Metabolic network often contains 'artifacts' that serve modelling purpose (to define a composite objective function for example). Such entities can be considered as 'side entities'. Since they are not actual chemical compounds, they can be detected by their lack of valid chemical formula. However, this can also flag main compounds with erroneous or missing annotation.]]></help> |
| 83 <citations/> | |
| 83 </tool> | 84 </tool> |