Mercurial > repos > iuc > scanpy_normalize

comparison macros.xml @ 15:f3ad813a58a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author iuc
date Wed, 31 Jul 2024 18:13:07 +0000
parents d844935c906c
children 9f354c7c8c92
comparison
equal deleted inserted replaced
14:d844935c906c 15:f3ad813a58a3
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>