Mercurial > repos > iuc > scanpy_remove_confounders
diff macros.xml @ 15:e66884b1c1a5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author | iuc |
---|---|
date | Wed, 31 Jul 2024 18:10:08 +0000 |
parents | c65fce500915 |
children | a39040ae0a38 |
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--- a/macros.xml Sat May 18 18:30:17 2024 +0000 +++ b/macros.xml Wed Jul 31 18:10:08 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.9.6</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@profile@">21.09</token> <xml name="requirements"> <requirements> @@ -425,6 +425,7 @@ <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" > <option value="all">All variables in 'adata.var_names'</option> <option value="custom">Subset of variables in 'adata.var_names'</option> + <option value="customfile">Subset of variables as a tabular file</option> </param> <when value="all"/> <when value="custom"> @@ -432,6 +433,9 @@ <expand macro="sanitize_query" /> </param> </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> + </when> </conditional> </xml> <xml name="param_num_categories"> @@ -468,11 +472,13 @@ <expand macro="param_num_categories"/> </xml> <token name="@CMD_params_inputs@"><![CDATA[ - #if $method.var_names.type == 'all' - var_names=adata.var_names, - #else + #if $method.var_names.type == 'custom' #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) var_names=$var_names, + #else if $method.var_names.type == 'customfile' + var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()}, + #else + var_names=adata.var_names, #end if #if $method.groupby groupby='$method.groupby', @@ -1122,7 +1128,7 @@ </param> </xml> <xml name="param_n_genes"> - <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> + <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/> </xml> <xml name="pl_dotplot"> <param argument="color_map" type="select" optional="true" label="Color palette">