Adds PySCENIC wrappers #328
Conversation
There was a problem hiding this comment.
This should not be needed anymore.
There was a problem hiding this comment.
Do you have now a mechanism on IUC Tools to retrieve data for tests instead of leaving them on the repo? That is great!
There was a problem hiding this comment.
https://docs.galaxyproject.org/en/latest/dev/schema.html#id104 check out the location tag.
| <param name="expression_mtx_fname" format="loom" type="data" label="Expression Matrix File" help="The file that contains the expression matrix for the single-cell experiment. Supported formats: csv (rows=cells x columns=genes) or loom (rows=genes x columns=cells)." /> | ||
| <param name="signatures_fname" type="data" format="csv,tabular" label="Gene Signatures/Regulons File" help="The file that contains the gene signatures (usually the precomputed regulons). Currently only csv/tsv supported, could be extended." /> | ||
| <param name="transpose" type="boolean" label="Transpose Expression Matrix" help="Transpose the expression matrix if supplied as csv (rows=genes x columns=cells)." optional="true" /> | ||
| <param name="weights" type="boolean" label="Use Weights for Recovery Analysis" help="Use weights associated with genes in recovery analysis. Relevant when gene signatures are supplied as json format." optional="true" /> |
There was a problem hiding this comment.
add truevalue ... like below?
Co-authored-by: Björn Grüning <[email protected]>
|
Thanks for taking a look @bgruening |
| <param name="weights" type="boolean" label="Use Weights for Recovery Analysis" help="Use weights associated with genes in recovery analysis. Relevant when gene signatures are supplied as json format." optional="true"/> | ||
| <param name="seed" type="integer" label="Seed for Ranking" help="Seed for the expression matrix ranking step. The default is to use a random seed." optional="true"/> | ||
| <param name="rank_threshold" type="integer" label="Rank Threshold" help="The rank threshold used for deriving the target genes of an enriched motif (default: 5000)." optional="true"/> | ||
| <param name="auc_threshold" type="float" label="AUC Threshold" help="The threshold used for calculating the AUC of a feature as fraction of ranked genes (default: 0.05)." optional="true"/> |
There was a problem hiding this comment.
add min/max if you can to all floats/int
There was a problem hiding this comment.
A great suggestion, but I'm going to pass on this one, goes beyond the amount of time I can put to this. If anyone wants it dearly, the contribution will be welcome.
| </tests> | ||
| <help> | ||
| <
Description
Adds the PySCENIC wrappers for grn, ctx and aucell.
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).