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Feature/add met frag #2098
Feature/add met frag #2098
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categories: | ||
- Metabolomics | ||
description: MetFrag performs annotation of tandem mass spectra of metabolites. Candidate molecules of different databases are fragmented in silico and matched against mass MS/MS spectra. | ||
homepage_url: http://c-ruttkies.github.io/MetFrag/ | ||
name: metfrag | ||
owner: iuc | ||
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metfrag/ |
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<?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"> | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Can we use |
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<description>Run MetFrag with a given parameter set.</description> | ||
<requirements> | ||
<requirement type="package" version="2.4.5">metfrag</requirement> | ||
</requirements> | ||
<!-- | ||
#if $additionalparameters != "None" | ||
-a "$additionalparameters" | ||
#end if | ||
#if $additional_metfrag_scores != "None" | ||
-s "$additional_metfrag_scores" | ||
#end if | ||
--> | ||
<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" | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. indentation and single quotes :) |
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#end if | ||
]]> | ||
</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" /> | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 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? |
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<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"> | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. a select with only one option looks wired, do you want to use a boolean here? |
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<option value="OfflineMetFusionScore">Spectral Similarity (MoNA)</option> | ||
</param> | ||
</inputs> | ||
<outputs> | ||
<data name="metfrag_cli_batch_output_1" format="csv" label="MetFrag result file" /> | ||
</outputs> | ||
<tests> | ||
<test> | ||
<param name="metfrag_cli_batch_input_1" value="1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt" /> | ||
<param name="metfrag_cli_batch_database_file" value="candidates.csv" /> | ||
<output name="metfrag_cli_batch_output_1" file="1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv" ftype="csv"/> | ||
</test> | ||
</tests> | ||
<help> | ||
|
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.. class:: infomark | ||
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| **Tool update: See the 'NEWS' section at the bottom of the page** | ||
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--------------------------------------------------- | ||
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.. class:: infomark | ||
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**Authors** | ||
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| **Payam Emami ([email protected])** and **Christoph Ruttkies ([email protected])** wrote and maintain this wrapper for MetFrag batch mode processing. | ||
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--------------------------------------------------- | ||
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.. class:: infomark | ||
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**Please cite** | ||
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Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. and Neumann, S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8:3, (2016) DOI: 10.1186/s13321-016-0115-9 | ||
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--------------------------------------------------- | ||
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===================== | ||
MetFrag CLI Batch | ||
===================== | ||
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----------- | ||
Description | ||
----------- | ||
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| This module is used to run MetFrag on annotated MS/MS spectra for compound annotation. The parameters are set by **msms2metfrag**. | ||
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----------- | ||
Input files | ||
----------- | ||
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+------------------------------+------------+ | ||
| File | Format | | ||
+==============================+============+ | ||
| 1) File with MetFrag | txt | | ||
| parameters | | | ||
+------------------------------+------------+ | ||
| 2) Database File (optional) | csv | | ||
+------------------------------+------------+ | ||
|
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---------- | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. These parameter description does not add more information as the above help text. It would be nice if we can add additional information here. |
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Parameters | ||
---------- | ||
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File with MetFrag parameters | ||
| File containing MetFrag parameters which is generated by **msms2metfrag** | ||
| | ||
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Additional Parameters | ||
| 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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Database File | ||
| File containing candidates used as database | ||
| | ||
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Additional MetFrag scores | ||
| Add additional MetFrag scores used to score candidates | ||
| | ||
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------------ | ||
Output files | ||
------------ | ||
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metfrag_cli_batch_output_1.csv | ||
| A csv output file with scored candidates and properties | ||
| | ||
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--------------------------------------------------- | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. We do not list news or changes in a tool. This can be done in an additional readme file if you like. |
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---- | ||
NEWS | ||
---- | ||
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CHANGES IN VERSION 0.3 | ||
======================== | ||
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- added support for additional MetFrag scores | ||
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CHANGES IN VERSION 0.2 | ||
======================== | ||
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- added support for a local file database | ||
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CHANGES IN VERSION 0.1 | ||
======================== | ||
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First version | ||
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</help> | ||
<citations> | ||
<citation type="doi">10.1186/s13321-016-0115-9</citation> | ||
</citations> | ||
</tool> | ||
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<!-- Local Variables: --> | ||
<!-- nxml-child-indent: 4 --> | ||
<!-- nxml-attribute-indent: 4 --> | ||
<!-- End: --> |
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can we remove these comments?
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Gone.