Mercurial > repos > ebi-gxa > anndata_ops
changeset 4:34a9d77a558d draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"
author | ebi-gxa |
---|---|
date | Fri, 12 Jun 2020 12:40:20 +0000 |
parents | 8705f7333bdf |
children | |
files | anndata_operations.xml |
diffstat | 1 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/anndata_operations.xml Thu Jun 11 16:59:50 2020 +0000 +++ b/anndata_operations.xml Fri Jun 12 12:40:20 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy0" profile="@PROFILE@"> +<tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy1" profile="@PROFILE@"> <description>modifies metadata and flags genes</description> <macros> <import>scanpy_macros2.xml</import> @@ -36,6 +36,10 @@ adata = sc.read('input.h5') +#if $copy_adata_to_raw: +adata.raw = adata +#end if + gene_name = '${gene_symbols_field}' qc_vars = list() @@ -128,6 +132,7 @@ <inputs> <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/> <expand macro="output_object_params_no_loom"/> + <param name="copy_adata_to_raw" type="boolean" label="Copy AnnData to .raw" help="If activated, it will do 'adata.raw = adata'" checked="false"/> <repeat name="modifications" title="Change field names in AnnData observations" min="0"> <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change"> <sanitizer>