add pgxRpi tool #6805
add pgxRpi tool #6805
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Co-authored-by: Khaled196 <[email protected]>
Co-authored-by: Khaled196 <[email protected]>
Co-authored-by: Khaled196 <[email protected]>
tools/pgxRpi/pgxFreqplot.xml
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| @@ -0,0 +1,80 @@ | |||
| <tool id="pgx_freqplot" name="pgxRpi pgxFreqplot" version="0.1.0+galaxy0" profile="21.05"> | |||
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should the version 1.20 and maybe a macro?
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Thank you for pointing this out. I have included it in a macro.
tools/pgxRpi/pgxFreqplot.xml
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| <option value="hg38" selected="true">hg38</option> | ||
| <option value="hg19">hg19</option> | ||
| </param> | ||
| <param name='plotwidth' type='integer' value='8' label='Width of the plot in inches.' /> |
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Can we use a proper metric system here ;) I propose cm or mm ;)
tools/pgxRpi/pgxFreqplot.xml
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| <help><![CDATA[ | ||
| Thie function plots the CNV frequency loaded from pgxRpi | ||
| ]]></help> | ||
| <citations> |
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I have placed the citation in a macro. However, since the help text varies across different functions, I have not included it in a macro.
tools/pgxRpi/pgxLoader.xml
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| </param> | ||
| <param name='limit' type='integer' value='0' optional='true' label='Integer to specify the number of returned profiles' /> | ||
| <param name='skip' type='integer' value='0' optional='true' label='Integer specifying the number of profiles to skip' /> | ||
| <param name='dataset' type='text' optional='true' label='Dataset to query from the Beacon response' help='Use commas to separate multiple datasets to enter' /> |
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How should such a text look like? Is it really a dataset?
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This parameter is used to select specific datasets for Progenetix. Currently, Progenetix returns data using only one dataset ID, "progenetix." I have updated the default value of this parameter to "progenetix."
The reason for keeping this parameter is that the package can also query data from other resources via the Beacon API, where "dataset" is a standard query parameter. This allows for more flexible queries across different resources and supports future expansions of Progenetix.
| <data name="pgxdata" format="txt" label="${tool.name} for $type data" /> | ||
| </outputs> | ||
| <tests> | ||
| <test> |
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please add tests with more options, especially from the advanced settings
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Thank you for your suggestions! I have included several tests covering different input types and advanced settings.
However, a few input types, such as “sample_counts,” are not included because these queries return aggregated results. Since Progenetix data is continuously expanding, the results may change over time, causing test failures despite the tool functioning correctly.
Similarly, some parameters, such as “filters,” are not included because their queries return multiple records in a non-fixed order, which could lead to test failures.
| <option value="sample_count">count of samples in Progenetix</option> | ||
| <option value="filtering_terms">All available filters in Progenetix</option> | ||
| </param> | ||
| <param name='biosample_id' type='text' optional='true' label='Identifiers of biosamples' help='Use commas to separate multiple IDs (e.g. pgxbs-m3io46hq,pgxbs-m3io41c2). If the output data type is "genomic variations", only this search condition is supported.' /> |
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it would be nice to add some validators to all those text inputs
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Please refer to my response above
Co-authored-by: Björn Grüning <[email protected]>
FOR CONTRIBUTOR:
This PR adds a Galaxy wrapper for pgxRpi, a package that provides a streamlined interface to the Progenetix Beacon v2 API to facilitate efficient and flexible retrieval of genomic variation data.