Mercurial > repos > iuc > scanpy_filter
comparison macros.xml @ 15:aa0059118fb9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author | iuc |
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date | Wed, 31 Jul 2024 18:10:52 +0000 |
parents | d636ce5cde16 |
children | 72a6bebab2a5 |
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14:d636ce5cde16 | 15:aa0059118fb9 |
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1 <macros> | 1 <macros> |
2 <token name="@TOOL_VERSION@">1.9.6</token> | 2 <token name="@TOOL_VERSION@">1.9.6</token> |
3 <token name="@VERSION_SUFFIX@">3</token> | 3 <token name="@VERSION_SUFFIX@">4</token> |
4 <token name="@profile@">21.09</token> | 4 <token name="@profile@">21.09</token> |
5 <xml name="requirements"> | 5 <xml name="requirements"> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> | 7 <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> |
8 <requirement type="package" version="3.0.6">loompy</requirement> | 8 <requirement type="package" version="3.0.6">loompy</requirement> |
423 <xml name="pl_var_names"> | 423 <xml name="pl_var_names"> |
424 <conditional name="var_names"> | 424 <conditional name="var_names"> |
425 <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" > | 425 <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" > |
426 <option value="all">All variables in 'adata.var_names'</option> | 426 <option value="all">All variables in 'adata.var_names'</option> |
427 <option value="custom">Subset of variables in 'adata.var_names'</option> | 427 <option value="custom">Subset of variables in 'adata.var_names'</option> |
428 <option value="customfile">Subset of variables as a tabular file</option> | |
428 </param> | 429 </param> |
429 <when value="all"/> | 430 <when value="all"/> |
430 <when value="custom"> | 431 <when value="custom"> |
431 <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma"> | 432 <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma"> |
432 <expand macro="sanitize_query" /> | 433 <expand macro="sanitize_query" /> |
433 </param> | 434 </param> |
435 </when> | |
436 <when value="customfile"> | |
437 <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> | |
434 </when> | 438 </when> |
435 </conditional> | 439 </conditional> |
436 </xml> | 440 </xml> |
437 <xml name="param_num_categories"> | 441 <xml name="param_num_categories"> |
438 <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/> | 442 <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/> |
466 <expand macro="pl_var_names"/> | 470 <expand macro="pl_var_names"/> |
467 <expand macro="param_groupby"/> | 471 <expand macro="param_groupby"/> |
468 <expand macro="param_num_categories"/> | 472 <expand macro="param_num_categories"/> |
469 </xml> | 473 </xml> |
470 <token name="@CMD_params_inputs@"><![CDATA[ | 474 <token name="@CMD_params_inputs@"><![CDATA[ |
471 #if $method.var_names.type == 'all' | 475 #if $method.var_names.type == 'custom' |
472 var_names=adata.var_names, | |
473 #else | |
474 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) | 476 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) |
475 var_names=$var_names, | 477 var_names=$var_names, |
478 #else if $method.var_names.type == 'customfile' | |
479 var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()}, | |
480 #else | |
481 var_names=adata.var_names, | |
476 #end if | 482 #end if |
477 #if $method.groupby | 483 #if $method.groupby |
478 groupby='$method.groupby', | 484 groupby='$method.groupby', |
479 #end if | 485 #end if |
480 num_categories=$method.num_categories, | 486 num_categories=$method.num_categories, |
1120 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols"> | 1126 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols"> |
1121 <expand macro="sanitize_query" /> | 1127 <expand macro="sanitize_query" /> |
1122 </param> | 1128 </param> |
1123 </xml> | 1129 </xml> |
1124 <xml name="param_n_genes"> | 1130 <xml name="param_n_genes"> |
1125 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> | 1131 <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"/> |
1126 </xml> | 1132 </xml> |
1127 <xml name="pl_dotplot"> | 1133 <xml name="pl_dotplot"> |
1128 <param argument="color_map" type="select" optional="true" label="Color palette"> | 1134 <param argument="color_map" type="select" optional="true" label="Color palette"> |
1129 <expand macro="matplotlib_pyplot_colormap"/> | 1135 <expand macro="matplotlib_pyplot_colormap"/> |
1130 </param> | 1136 </param> |