scanpy qc plots #312
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scanpy qc plots #312
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pcm32
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Feb 8, 2024
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| <param type="text" name="sample_field" label="Sample Field" /> | ||
| <param type="select" name="output_format" label="Output Format"> | ||
| <option value="pdf">PDF</option> | ||
| <option value="png">PNG</option> | ||
| </param> | ||
| <param type="text" name="plot_size" label="Plot Size (Width Height)" value="10,10"/> | ||
| <param type="text" name="percent_mito_field" label="Mitochondrial Gene Field" /> | ||
| <param type="text" name="percent_ribo_field" label="Ribosomal Gene Field" /> | ||
| <param type="text" name="ribo_field" label="Ribo Field" /> | ||
| <param type="text" name="mito_field" label="Mito Field" /> | ||
| <param type="text" name="doublet_score_field" label="Doublet Score Field" /> |
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Please add a help field on each, explaining what they are. For example, for Mitochondrial Gene Field:
<param ... help="This is the field in the andata.obs pandas dataframe where the mitochondrial status of a gene is stored, usually mito"/>
pcm32
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Feb 8, 2024
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| <data name="general_qc_plots" format="pdf" label="General QC Plots" /> | ||
| <!-- Add more output parameters as needed --> |
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We need to add all the outputs (pdf or pngs) of the script. It is more entries in the part.
The reference for how to add outputs is here.
|
Example of results that need to be captured in the output part:
|
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Description
Introducing some additional QC plots for scanpy.
Fixes # (issue)
Type of change
Checklist
@TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g.@TOOL_VERSION@+galaxy0)@TOOL_VERSION@+galaxy0@TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).@TOOL_VERSION@part of the version does not contain any+symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only+should be the one precedinggalaxy<build>(unless that all the versions from that tool previously followed a different pattern).