New Scripting Nodes
A couple new scripting nodes can be found here.
- Adding an m/z column to the Compounds table
- Adding m/z and Delta Mass [ppm] columns to the Expected Compounds table
- Calculate O/C and H/C ratios in the Compounds table
- Show KEGG IDs (top mzCloud hit) in the Compounds table
Your feedback and requests for additional scripting nodes are welcome!
Posted on April 7, 2020, in Uncategorized. Bookmark the permalink. 8 Comments.
Hi Ralf, that’s very nice, I remember asking for the mz column and the theoretical logP vs RT plot.
My CD3.1 will not allow me to have more than one scripting node in my workflow… Is there a plan to allow several? Or am I missing something?
Hi Julie, great question. I’m happy you like the Scripting nodes. You are right, you can only use one Scripting node in the workflow. The Scripting node offers a convenient user interface that helps with the initial development and testing of a script. However once you are happy with your script, you can then “install” your Scripting node as a standalone node which looks just like all the other nodes. That way you can install and use as many Scripting nodes as you want and you can also use additional options like having menu options in the node parameters to pass these additional parameters to the node etc. The installation process is described in section “Registering Standalone Scripting Nodes” in the Custom Script Integration manual and you can find an example for the JSON file that is required in SimpleTest.zip (Example 1). I was thinking about creating the JSON files also for the other examples but the file paths within those JSON files would still need to be adjusted for your R version and location of the script. Please let me know if you need help with the JSON files or the installation process!
Thank you for the quick reply.
Anas suggested that maybe I could put the code of several desired scripting nodes into a single longer code then used in the single scripting node in the workflow. Would that work? I’m just wondering if the variable description part would be easy enough and would not create conflicts. I haven’t tried yet anyway.
Anas is right. That would work too. However it would require a significant rewriting of the code, whereas the other solution (install as standalone scripting nodes) only requires the JSON file for the installation to be created. I can help with that if needed, just send me a email.
I’ve noticed a minor error in the scripts for CompoundsMZ and ExpectedCompoundsMZDeltaPPM when using with CD3.2. The m/z column is supposed to follow the Molecular Weight column, but that column can’t be found, so the script just puts it at the end of the Table.
Is there a Table Name and Column Name Listing for CD3.2 like there is for Proteome Discoverer.
Is there a way to have a default ordering of the Tables and Columns to be displayed in the result fie?
thank you for pointing that out. Most of the Scripting node examples were written when CD3.1 was released. Some columns were renamed or have changed for the CD3.2 release (e.g. “Molecular Weight” is now “Calc. MW”) that is why you see this error. Since it was requested quite frequently we will add m/z columns (together with new options for the relative quantitation) for the CD3.3 release anyway so these two nodes will be obsolete soon. There is currently no complete listing of Tables and Columns but we will consider it for the next release.
I have tried to execute the scripting node logP as described in the document on logP.R (05/13/2020 Ralf Tautenhahn) but I used to receive the following error:
”Error The executable ran for 1 s and finished with error(s), exit code was:-1073741819”
I am using CD 3.3 for suspect screening of organic contaminants.
I hope you can help.
a lot of the scripts were written for older versions of CD and have not been updated yet for 3.3. Some of the column names in the Compounds table have changed in 3.3. That is probably the reason for the error message. I’ll follow up with you per email.