Mercurial > repos > ebi-gxa > anndata_ops
changeset 11:f0a29f4b9be9 draft
"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 09:19:22 -0400 |
| parents | 54f1212d26ac |
| children | f1a1cf7c0153 |
| files | anndata_operations.xml |
| diffstat | 1 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/anndata_operations.xml Thu Jun 11 13:07:33 2020 -0400 +++ b/anndata_operations.xml Fri Jun 12 09:19:22 2020 -0400 @@ -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>