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galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
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Thermo raw file parser outputname #629

Closed jj-umn closed 3 years ago

jj-umn commented 3 years ago

@subinamehta requested the the input spectrum name be preserved when using ThermoRawConverter.
This will remove a .raw or .RAW extension from the input name and append either a .mgf or .mzml as the output name.

subinamehta commented 3 years ago

So tags help in us figuring out the file name. In the case of a tabular output that contains a column with the filename, this naming will cause a problem. I just wanted the tool to name the output as input_file_name.mgf or input_file_name.mzml rather than Thermo on data1.

On Wed, Aug 25, 2021 at 12:41 PM Björn Grüning @.***> wrote:

@.**** commented on this pull request.

In tools/ThermoRawFileParser/thermo_converter.xml https://github.com/galaxyproteomics/tools-galaxyp/pull/629#discussion_r695928466 :

@@ -85,7 +85,7 @@ ThermoRawFileParser.sh

- +

I don't think we should do such magic. Its a Galaxy issue, that we should not fix per tool. The way we recommend today is using tags. Do tags help here? @subinamehta https://github.com/subinamehta ?

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bgruening commented 3 years ago

Can you use collections? Then the names stays like input_file_name.mgf

subinamehta commented 3 years ago

Can you use collections? Then the names stays like input_file_name.mgf I guess that we can do, the issue still remains though when there is only one file involved.

bgruening commented 3 years ago

One file can also be in one collection :)