# HG changeset patch # User tduigou # Date 1639417242 0 # Node ID ea2ca40a24c50b7f4a919da2ba27560cf670925b "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" diff -r 000000000000 -r ea2ca40a24c5 rpviz.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz.xml Mon Dec 13 17:40:42 2021 +0000 @@ -0,0 +1,101 @@ + + Visualize pathways from the RetroPath Suite + + rptools + + + + + + + + + + + + + + + + + + + +
+ +
+ + + + + + + + + + + + + + + + + + + + + + + `_ + +Version +---------- + +5.10.0 + +License +------- + +* `MIT `_ + + ]]> + \ No newline at end of file diff -r 000000000000 -r ea2ca40a24c5 test-data/as_tar_inputs.tgz Binary file test-data/as_tar_inputs.tgz has changed diff -r 000000000000 -r ea2ca40a24c5 test-data/lycopene_CrtEBI_from_selenzy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lycopene_CrtEBI_from_selenzy.xml Mon Dec 13 17:40:42 2021 +0000 @@ -0,0 +1,532 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r ea2ca40a24c5 test-data/rpviz_single_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rpviz_single_output.html Mon Dec 13 17:40:42 2021 +0000 @@ -0,0 +1,6560 @@ + + + + + + + + + + Pathway viewer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+
+
+
Pathway selection
+
+
+ +
+ + + +
+
+
Cofactor options
+
+ + +
+
+
+
+
+
+ +
+
Legend
+
How to
+ +
1/ Pass the mouse hover pathway IDs (the "Pathway" column in the left table) to emphasize a specific path.
+
2/ Click once on a pathway ID (in the left table) to "pin" a path. When at least one pathway is pinned, + other pathways are faded.Click a second time on a pinned pathway ID to unpin it.
+
3/ Mark / unmark the checkboxes (the "Show" column in the left table) to select which pathways are visible.
+
4/ Cofactors are hidden by default. One can use the "Show cofactors" and "Hide cofactors" button to change this display.
+
5/ Click on the icon (in the left table) to visualise information about a pathway
+
6/ Click on a node to visualise information about chemicals and reactions
+
Node shape
+
+

▢ Chemical

+

◯ Transformation (in/outgoing arrows show direction)

+
+
Compound color
+
+

▢ Target

+

▢ Intermediate chemicals

+

▢ Precursors

+
+
+ +
+
Chemical
+
+
+ +
+
+
+
+
+ +
+
SMILES
+
+
+
+ +
+
InChI
+
+
+
+ +
+
InChIKey
+
+
+
+ +
+
Is a cofactor?
+
+
+ +
+
Is a precursor?
+
+
+ +
+
Crosslinks
+
+
+ +
+
Pathways involved in
+
+
+
+ +
+
Reaction
+
+
+ +
+
EC number(s)
+
+
+ +
+
Crosslinks
+
+
+ +
+
ΔrG' (kJ/mol)
+
+
+ +
+
Rule score
+
+
+ +
+
Reaction SMILES
+
+
+ +
+
Rule ID(s)
+
+
+ +
+
Reaction template ID(s)
+
+
+ +
+
Pathways involved in
+
+
+ +
+
UniProt IDs (Selenzyme score)
+
+
+ +
+
Enzyme selection
+
+
+
+ +
+
Pathway
+
+
+ +
+
Pathway ID
+
+
+ +
+
Number of steps
+
+
+ +
+
ΔrG' (kJ/mol)
+
+
+ +
+
Rule score
+
+
+ +
+
Target's production flux (mmol gDW-1 hr-1)
+
+
+ +
+
Global score
+
+
+
+ + +
+ +
+
+ +
+ + + diff -r 000000000000 -r ea2ca40a24c5 test-data/rpviz_tar_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rpviz_tar_output.html Mon Dec 13 17:40:42 2021 +0000 @@ -0,0 +1,7436 @@ + + + + + + + + + + Pathway viewer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+
+
+
Pathway selection
+
+
+ +
+ + + +
+
+
Cofactor options
+
+ + +
+
+
+
+
+
+ +
+
Legend
+
How to
+ +
1/ Pass the mouse hover pathway IDs (the "Pathway" column in the left table) to emphasize a specific path.
+
2/ Click once on a pathway ID (in the left table) to "pin" a path. When at least one pathway is pinned, + other pathways are faded.Click a second time on a pinned pathway ID to unpin it.
+
3/ Mark / unmark the checkboxes (the "Show" column in the left table) to select which pathways are visible.
+
4/ Cofactors are hidden by default. One can use the "Show cofactors" and "Hide cofactors" button to change this display.
+
5/ Click on the icon (in the left table) to visualise information about a pathway
+
6/ Click on a node to visualise information about chemicals and reactions
+
Node shape
+
+

▢ Chemical

+

◯ Transformation (in/outgoing arrows show direction)

+
+
Compound color
+
+

▢ Target

+

▢ Intermediate chemicals

+

▢ Precursors

+
+
+ +
+
Chemical
+
+
+ +
+
+
+
+
+ +
+
SMILES
+
+
+
+ +
+
InChI
+
+
+
+ +
+
InChIKey
+
+
+
+ +
+
Is a cofactor?
+
+
+ +
+
Is a precursor?
+
+
+ +
+
Crosslinks
+
+
+ +
+
Pathways involved in
+
+
+
+ +
+
Reaction
+
+
+ +
+
EC number(s)
+
+
+ +
+
Crosslinks
+
+
+ +
+
ΔrG' (kJ/mol)
+
+
+ +
+
Rule score
+
+
+ +
+
Reaction SMILES
+
+
+ +
+
Rule ID(s)
+
+
+ +
+
Reaction template ID(s)
+
+
+ +
+
Pathways involved in
+
+
+ +
+
UniProt IDs (Selenzyme score)
+
+
+ +
+
Enzyme selection
+
+
+
+ +
+
Pathway
+
+
+ +
+
Pathway ID
+
+
+ +
+
Number of steps
+
+
+ +
+
ΔrG' (kJ/mol)
+
+
+ +
+
Rule score
+
+
+ +
+
Target's production flux (mmol gDW-1 hr-1)
+
+
+ +
+
Global score
+
+
+
+ + +
+ +
+
+ +
+ + +