Mercurial > repos > ebi-gxa > scanpy_find_variable_genes
changeset 21:79da59a0b180 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 69b3fd29988bdcbf30d38572b75793ab74110acd-dirty"
| author | ebi-gxa |
|---|---|
| date | Fri, 06 Aug 2021 15:22:46 +0000 |
| parents | 24fca62faafd |
| children | 82bd7bf93454 |
| files | scanpy-find-variable-genes.xml |
| diffstat | 1 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/scanpy-find-variable-genes.xml Tue Aug 03 08:59:02 2021 +0000 +++ b/scanpy-find-variable-genes.xml Fri Aug 06 15:22:46 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>based on normalised dispersion of expression</description> <macros> <import>scanpy_macros2.xml</import> @@ -23,6 +23,9 @@ #end if --n-bins '${n_bin}' ${filter} +#if $batch_key + --batch-key ${batch_key} +#end if @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> @@ -50,7 +53,7 @@ <param name="n_bin" argument="--n-bins" type="integer" value="20" label="Number of bins for binning the mean expression"/> <param name="filter" argument="--subset" type="boolean" truevalue="--subset" falsevalue="" checked="false" label="Remove genes not marked as highly variable" help="When set, inplace subset to highly-variable genes, otherwise only flag highly-variable genes."/> - <param name="batch_key" argument="--batch-key" type="text" label="Batch key" help="If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties are broken by the median (across batches) rank based on within-batch normalized variance."/> + <param name="batch_key" argument="--batch-key" type="text" label="Batch key" optional="true" help="If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. For all flavors, genes are first sorted by how many batches they are a HVG. For dispersion-based flavors ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties are broken by the median (across batches) rank based on within-batch normalized variance."/> </inputs> <outputs>