Mercurial > repos > iuc > scanpy_inspect

comparison inspect.xml @ 12:3081ff5c84a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
author iuc
date Fri, 17 Nov 2023 09:15:15 +0000
parents 6bd82ed14acd
children f54f0f0598ad
comparison
equal deleted inserted replaced
11:6bd82ed14acd 12:3081ff5c84a3
1 <tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@"> 1 <tool id="scanpy_inspect" name="Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
2 <description> with scanpy</description> 2 <description> with scanpy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="score_genes_params"> 5 <xml name="score_genes_params">
6 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/> 6 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/>
64 #if $method.method == "pp.calculate_qc_metrics" 64 #if $method.method == "pp.calculate_qc_metrics"
65 sc.pp.calculate_qc_metrics( 65 sc.pp.calculate_qc_metrics(
66 adata=adata, 66 adata=adata,
67 expr_type='$method.expr_type', 67 expr_type='$method.expr_type',
68 var_type='$method.var_type', 68 var_type='$method.var_type',
69 #if str($method.qc_vars) != '' 69 #if $method.qc_vars
70 #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')] 70 #set $qc_vars = [str(x.strip()) for x in str($method.qc_vars).split(',')]
71 qc_vars=$qc_vars, 71 qc_vars=$qc_vars,
72 #end if 72 #end if
73 #if str($method.percent_top) != '' 73 #if $method.percent_top
74 #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')] 74 #set $percent_top = [int(x.strip()) for x in str($method.percent_top).split(',')]
75 percent_top=$method.percent_top, 75 percent_top=$method.percent_top,
76 #end if 76 #end if
77 inplace=True) 77 inplace=True)
78 78
123 adata=adata, 123 adata=adata,
124 n_neighbors=$method.n_neighbors, 124 n_neighbors=$method.n_neighbors,
125 #if str($method.n_pcs) != '' 125 #if str($method.n_pcs) != ''
126 n_pcs=$method.n_pcs, 126 n_pcs=$method.n_pcs,
127 #end if 127 #end if
128 #if str($method.use_rep) != '' 128 #if $method.use_rep
129 use_rep='$method.use_rep', 129 use_rep='$method.use_rep',
130 #end if 130 #end if
131 knn=$method.knn, 131 knn=$method.knn,
132 random_state=$method.random_state, 132 random_state=$method.random_state,
133 method='$method.pp_neighbors_method', 133 method='$method.pp_neighbors_method',
136 136
137 #else if $method.method == 'tl.rank_genes_groups' 137 #else if $method.method == 'tl.rank_genes_groups'
138 sc.tl.rank_genes_groups( 138 sc.tl.rank_genes_groups(
139 adata=adata, 139 adata=adata,
140 groupby='$method.groupby', 140 groupby='$method.groupby',
141 #if str($method.groups) != '' 141 #if $method.groups
142 #set $group=[x.strip() for x in str($method.groups).split(',')] 142 #set $group=[x.strip() for x in str($method.groups).split(',')]
143 groups=$group, 143 groups=$group,
144 #end if 144 #end if
145 #if $method.ref.rest == 'rest' 145 #if $method.ref.rest == 'rest'
146 reference='$method.ref.rest', 146 reference='$method.ref.rest',
174 #end if 174 #end if
175 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept, 175 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept,
176 #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True' 176 #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'
177 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling, 177 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
178 #end if 178 #end if
179 #if $method.tl_rank_genes_groups_method.solver.random_state 179 #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
180 random_state=$method.tl_rank_genes_groups_method.solver.random_state, 180 random_state=$method.tl_rank_genes_groups_method.solver.random_state,
181 #end if 181 #end if
182 #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag' 182 #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'
183 penalty='l2', 183 penalty='l2',
184 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept, 184 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
185 #if $method.tl_rank_genes_groups_method.solver.random_state 185 #if str($method.tl_rank_genes_groups_method.solver.random_state) != ''
186 random_state=$method.tl_rank_genes_groups_method.solver.random_state, 186 random_state=$method.tl_rank_genes_groups_method.solver.random_state,
187 #end if 187 #end if
188 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter, 188 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
189 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class', 189 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
190 #else if $method.tl_rank_genes_groups_method.solver.solver == 'saga' 190 #else if $method.tl_rank_genes_groups_method.solver.solver == 'saga'
211 #end for 211 #end for
212 212
213 sc.tl.marker_gene_overlap( 213 sc.tl.marker_gene_overlap(
214 adata, 214 adata,
215 reference_markers, 215 reference_markers,
216 #if str($method.key) != '' 216 #if $method.key
217 key='$method.key', 217 key='$method.key',
218 #end if 218 #end if
219 method='$method.overlap.method', 219 method='$method.overlap.method',
220 #if $method.overlap.method == 'overlap_count' and str($method.overlap.normalize) != 'None' 220 #if $method.overlap.method == 'overlap_count' and str($method.overlap.normalize) != 'None'
221 normalize='$method.overlap.normalize', 221 normalize='$method.overlap.normalize',
224 top_n_markers=$method.top_n_markers, 224 top_n_markers=$method.top_n_markers,
225 #end if 225 #end if
226 #if str($method.adj_pval_threshold) != '' 226 #if str($method.adj_pval_threshold) != ''
227 adj_pval_threshold=$method.adj_pval_threshold, 227 adj_pval_threshold=$method.adj_pval_threshold,
228 #end if 228 #end if
229 #if str($method.key_added) != '' 229 #if $method.key_added
230 key_added='$method.key_added', 230 key_added='$method.key_added',
231 #end if 231 #end if
232 inplace=True) 232 inplace=True)
233 233
234 #else if $method.method == "pp.log1p" 234 #else if $method.method == "pp.log1p"
238 238
239 #else if $method.method == "pp.scale" 239 #else if $method.method == "pp.scale"
240 sc.pp.scale( 240 sc.pp.scale(
241 adata, 241 adata,
242 zero_center=$method.zero_center, 242 zero_center=$method.zero_center,
243 #if $method.max_value 243 #if str($method.max_value) != ''
244 max_value=$method.max_value, 244 max_value=$method.max_value,
245 #end if 245 #end if
246 copy=False) 246 copy=False)
247 247
248 #else if $method.method == "pp.sqrt" 248 #else if $method.method == "pp.sqrt"
366 </when> 366 </when>
367 </conditional> 367 </conditional>
368 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/> 368 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
369 <conditional name="tl_rank_genes_groups_method"> 369 <conditional name="tl_rank_genes_groups_method">
370 <param argument="method" type="select" label="Method"> 370 <param argument="method" type="select" label="Method">
371 <option value="t-test">t-test</option> 371 <option value="t-test" selected="true">t-test</option>
372 <option value="wilcoxon">Wilcoxon-Rank-Sum</option> 372 <option value="wilcoxon">Wilcoxon-Rank-Sum</option>
373 <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option> 373 <option value="t-test_overestim_var">t-test with overestimate of variance of each group</option>
374 <option value="logreg">Logistic regression</option> 374 <option value="logreg">Logistic regression</option>
375 </param> 375 </param>
376 <when value="t-test"> 376 <when value="t-test">
377 <expand macro="corr_method"/> 377 <expand macro="corr_method"/>
378 </when> 378 </when>