Mercurial > repos > iuc > scanpy_filter
changeset 16:72a6bebab2a5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
| author | iuc |
|---|---|
| date | Tue, 20 Aug 2024 09:53:08 +0000 |
| parents | aa0059118fb9 |
| children | |
| files | filter.xml macros.xml test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png |
| diffstat | 6 files changed, 11 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/filter.xml Wed Jul 31 18:10:52 2024 +0000 +++ b/filter.xml Tue Aug 20 09:53:08 2024 +0000 @@ -524,7 +524,7 @@ <has_text_matching expression="adata, key, x, 1.0, 0.2, 'bulk_labels'"/> </assert_contents> </output> - <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" ftype="h5ad"> + <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad" ftype="h5ad"> <assert_contents> <has_h5_keys keys="obs, var, uns" /> </assert_contents>
--- a/macros.xml Wed Jul 31 18:10:52 2024 +0000 +++ b/macros.xml Tue Aug 20 09:53:08 2024 +0000 @@ -435,6 +435,10 @@ </when> <when value="customfile"> <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param> + <param name="header" type="select" label="Header in the list of markers?"> + <option value="included">Header incldued</option> + <option value="not_included">Header not included</option> + </param> </when> </conditional> </xml> @@ -471,6 +475,12 @@ <expand macro="param_groupby"/> <expand macro="param_num_categories"/> </xml> + <token name="@CMD_var_names_header_check@"><![CDATA[ +header='infer' +#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' : +header=None +#end if + ]]></token> <token name="@CMD_params_inputs@"><![CDATA[ #if $method.var_names.type == 'custom' #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
Binary file test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad has changed