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Feature/add met frag #2098

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Feature/add met frag #2098

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sneumann
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@sneumann sneumann commented Sep 21, 2018 •
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FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

FOR REVIEWER:

  • .shed.yml file ok
    • Toolshed user iuc has access to associated toolshed repo(s)
  • Indentation is correct (4 spaces)
  • Tool version/build ok
  • <command/>
    • Text parameters, input and output files 'single quoted'
    • Use of <![CDATA[ ... ]]> tags
    • Parameters of type text or having optional="true" attribute are checked with if str($param) before being used
  • Data parameters have a format attribute containing datatypes recognised by Galaxy
  • Tests
    • Parameters are reasonably covered
    • Test files are appropriate
  • Help
    • Valid restructuredText and uses <![CDATA[ ... ]]> tags
  • Complies with other best practice in Best Practices Doc

bgruening
bgruening reviewed Sep 23, 2018
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Thanks @sneumann!
I added a few comments. Please also consider to use tab-separated-files as Galaxy has a bunch of tools to process them without converting them in between.

tools/metfrag/metfrag-cli-batch.xml
@@ -0,0 +1,149 @@
<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/).-->
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can we remove these comments?

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Gone.

tools/metfrag/metfrag-cli-batch.xml
<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/).-->
<!--Proposed Tool Section: [PhenoMeNal]-->
<tool id="metfrag-cli-batch" name="metfrag-cli-batch" version="0.4">
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Can we use _ instead of - for the id?
I would also use Run MetFrag as name and the rest as a description.

tools/metfrag/metfrag-cli-batch.xml
<command detect_errors="aggressive"><![CDATA[
metfrag ParameterFile='$metfrag_cli_batch_input_1' ResultsFile='$metfrag_cli_batch_output_1'
#if $metfrag_cli_batch_database_file != "None"
LocalDatabasePath="$metfrag_cli_batch_database_file"
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indentation and single quotes :)

tools/metfrag/metfrag-cli-batch.xml
</command>
<inputs>
<param name="metfrag_cli_batch_input_1" type="data" format="txt" optional="False" label="File with MetFrag parameters" help="File containing MetFrag parameters which is generated by msms2metfrag" />
<param name="additionalparameters" type="text" value="" optional="True" label="Additional Parameters" help="Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance" />
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This can be very dangerous, as a user can pass everything to the command line. Are there too many parameters to explicitly list them here?

tools/metfrag/metfrag-cli-batch.xml
<param name="metfrag_cli_batch_input_1" type="data" format="txt" optional="False" label="File with MetFrag parameters" help="File containing MetFrag parameters which is generated by msms2metfrag" />
<param name="additionalparameters" type="text" value="" optional="True" label="Additional Parameters" help="Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance" />
<param name="metfrag_cli_batch_database_file" type="data" format="csv" optional="True" label="Database File" help="File containing candidates used as database" />
<param name="additional_metfrag_scores" type="select" display="checkboxes" multiple="true" label="Additional MetFrag scores" help="Add additional MetFrag scores used to score candidates">
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a select with only one option looks wired, do you want to use a boolean here?

tools/metfrag/metfrag-cli-batch.xml
| A csv output file with scored candidates and properties
|

---------------------------------------------------
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We do not list news or changes in a tool. This can be done in an additional readme file if you like.

tools/metfrag/metfrag-cli-batch.xml
| 2) Database File (optional) | csv |
+------------------------------+------------+

----------
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These parameter description does not add more information as the above help text. It would be nice if we can add additional information here.

@bernt-matthias
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@sneumann still needed in IUC? Seems that there are new recent plans: computational-metabolomics/metfrag-galaxy#9

@bernt-matthias
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I think we can close this now since metfrag is now in Galaxy https://github.com/computational-metabolomics/metfrag-galaxy. Or?

@sneumann
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sneumann commented Feb 8, 2021

Yes, happy to see it maintained as Galaxy tool. Thanks Ralf et al ! Yours, Steffen

@sneumann sneumann closed this Feb 8, 2021
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@sneumann @bernt-matthias @bgruening