| Previous changeset 15:aa0059118fb9 (2024-07-31) Next changeset 17:713a0c65b1fe (2024-09-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 |
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modified:
filter.xml macros.xml test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad |
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added:
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 |
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| diff -r aa0059118fb9 -r 72a6bebab2a5 filter.xml --- a/filter.xml Wed Jul 31 18:10:52 2024 +0000 +++ b/filter.xml Tue Aug 20 09:53:08 2024 +0000 |
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| @@ -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> |
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| diff -r aa0059118fb9 -r 72a6bebab2a5 macros.xml --- a/macros.xml Wed Jul 31 18:10:52 2024 +0000 +++ b/macros.xml Tue Aug 20 09:53:08 2024 +0000 |
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| @@ -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(',')]) |
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| diff -r aa0059118fb9 -r 72a6bebab2a5 test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad |
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| Binary file test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad has changed |
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| diff -r aa0059118fb9 -r 72a6bebab2a5 test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1_out.h5ad |
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| diff -r aa0059118fb9 -r 72a6bebab2a5 test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png |
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| Binary file test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png has changed |
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| diff -r aa0059118fb9 -r 72a6bebab2a5 test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png |
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| Binary file test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png has changed |
