Table toFile

Hi,

I developed a KNIME workflow for the post-processing of LCMS data, and I am trying to integrate the AccurateMass Search into it.

I though I would need the Table ToFile node to be able to feed my KNIME table into the AccurateMass Search, but I have no idea on how to configure the Table ToFile - the drop-down menu in the demangler tab is empty, and if I run the node I get the error: "failed to apply settings: Could not find an implementation for the previously selected mangler: "

Can anyone help me solve this?

Thanks,

Sonia

Hi Sonia,

yes, the TableToFile node only works for very specific file types that need to be registered in the source code of the plugin.

I assume that you are speaking of one of the TSV inputs for AccurateMassSearch?

In this case an easy workaround would be to use the CSV Writer, adjust the settings such that the table looks like one of our examples (esp. set the Separator in the Advanced Tab to tabs), then go to the FlowVariables Tab of its Configuration Dialog, export the created filename to a Variable by entering a variable name of your choice in the text field next to the entry "filename". Then connect the variable port (red connections from the upper right corner) of the CSVWriter node with the variable port (upper left corner) of an Input File node, go to its config dialog, Flow Variable tab, and select the created variable in the dropdown menu of the "FILENAME" entry.

Let me know if that works.

Cheers

Julianus 

Hi Julianus,

 

Thanks for your reply.

I tried what you suggested but unfortunately it does not work, it seems that the variable trick it is not enough to pass the information from the csv writer to the input file node as the latter requires a valid file selected.

I tried to overcome this by saving a .tsv file with the csv writer, loading it into KNIME with the input file node and using the FileConverter to obtain a featureXML file to feed to the AccurateMassSearch.

However, the FileConverter throws the error

ERROR FileConverter        0:719      Failing process stdout: [Warning: Parameters file version (2.3.0) does not match the version of this tool (2.1.0)., Error: Unable to read file (Failed to convert line 2. Not enough columns (expected 18 or more, got 16) in: )]
ERROR FileConverter        0:719      Failing process stderr: []
ERROR FileConverter        0:719      Execute failed: Failed to execute node FileConverter

 

Any idea of what it is happening?

Cheers,

Sonia

 

Hi Sonia

if you use FileConverter to convert TSV to featureXML, it expects MSInspect tsv format.
You can see under the following link, which columns correspond to which OpenMS data structures:

Cheers
Julianus