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comparison manipulate.xml @ 1:19592ec717ef draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:26:45 -0400
parents 0ef28c0963c8
children a56baceb1900
comparison
equal deleted inserted replaced
0:0ef28c0963c8 1:19592ec717ef
48 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')] 48 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
49 adata.rename_categories( 49 adata.rename_categories(
50 key='$manipulate.key', 50 key='$manipulate.key',
51 categories=$categories) 51 categories=$categories)
52 52
53 #else if $manipulate.function == 'transpose'
54 adata.transpose()
55
56 #else if $manipulate.function == 'strings_to_categoricals' 53 #else if $manipulate.function == 'strings_to_categoricals'
57 adata.strings_to_categoricals() 54 adata.strings_to_categoricals()
55
56 #else if $manipulate.function == 'transpose'
57 adata = adata.transpose()
58
59 #else if $manipulate.function == 'add_annotation'
60 import pandas as pd
61 extra_annot_t = pd.read_csv('$manipulate.new_annot', sep='\t').reset_index(drop=True)
62 #if $manipulate.var_obs == 'var'
63 var_index = adata.var_names
64 var = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1)
65 var.index = var_index
66 adata.var = var
67 #else if $manipulate.var_obs == 'obs'
68 obs_index = adata.obs.index
69 obs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1)
70 obs.index = obs_index
71 adata.obs = obs
72 #end if
73
74 #else if $manipulate.function == 'filter'
75 #if $manipulate.filter.filter == 'key'
76 #if $manipulate.var_obs == 'var'
77 filtered = adata.var['$manipulate.filter.key']
78 #else if $manipulate.var_obs == 'obs'
79 filtered = adata.obs['$manipulate.filter.key']
80 #end if
81
82 #if $manipulate.filter.filter_key.type == 'number'
83 #if $manipulate.filter.filter_key.filter == 'equal'
84 filtered = filtered == $manipulate.filter.filter_key.value
85 #else if $manipulate.filter.filter_key.filter == 'equal'
86 filtered = filtered != $manipulate.filter.filter_key.value
87 #else if $manipulate.filter.filter_key.filter == 'less'
88 filtered = filtered < $manipulate.filter.filter_key.value
89 #else if $manipulate.filter.filter_key.filter == 'less_or_equal'
90 filtered = filtered <= $manipulate.filter.filter_key.value
91 #else if $manipulate.filter.filter_key.filter == 'greater'
92 filtered = filtered > $manipulate.filter.filter_key.value
93 #else if $manipulate.filter.filter_key.filter == 'greater_or_equal'
94 filtered = filtered >= $manipulate.filter.filter_key.value
95 #end if
96 #else if $manipulate.filter.filter_key.type == 'text'
97 #if $manipulate.filter.filter_key.filter == 'equal'
98 filtered = filtered == '$manipulate.filter.filter_key.value'
99 #else
100 filtered = filtered != '$manipulate.filter.filter_key.value'
101 #end if
102 #else if $manipulate.filter.filter_key.type == 'boolean'
103 filtered = filtered == $manipulate.filter.filter_key.value
104 #end if
105
106 #else if $manipulate.filter.filter == 'index'
107 #if str($manipulate.filter.index.format) == 'file'
108 with open('$manipulate.filter.index.file', 'r') as filter_f:
109 filters = [str(x.strip()) for x in filter_f.readlines()]
110 filtered = filters
111 #else
112 #set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(',')]
113 filtered = $filters
114 #end if
115 #end if
116 print(filtered)
117
118 #if $manipulate.var_obs == 'var'
119 adata = adata[:,filtered]
120 #else if $manipulate.var_obs == 'obs'
121 adata = adata[filtered, :]
122 #end if
58 #end if 123 #end if
59 124
60 adata.write('anndata.h5ad') 125 adata.write('anndata.h5ad')
61 ]]></configfile> 126 ]]></configfile>
62 </configfiles> 127 </configfiles>
68 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option> 133 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
69 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option> 134 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
70 <option value="rename_categories">Rename categories of annotation</option> 135 <option value="rename_categories">Rename categories of annotation</option>
71 <option value="strings_to_categoricals">Transform string annotations to categoricals</option> 136 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
72 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option> 137 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
138 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
139 <option value="filter">Filter observations or variables</option>
73 </param> 140 </param>
74 <when value="concatenate"> 141 <when value="concatenate">
75 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/> 142 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
76 <param name="join" type="select" label="Join method"> 143 <param name="join" type="select" label="Join method">
77 <option value="inner">Intersection of variables</option> 144 <option value="inner">Intersection of variables</option>
95 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/> 162 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
96 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/> 163 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
97 </when> 164 </when>
98 <when value="strings_to_categoricals"/> 165 <when value="strings_to_categoricals"/>
99 <when value="transpose"/> 166 <when value="transpose"/>
167 <when value="add_annotation">
168 <param name="var_obs" type="select" label="What to annotate?">
169 <option value="var">Variables (var)</option>
170 <option value="obs">Observations (obs)</option>
171 </param>
172 <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
173 help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
174 </when>
175 <when value="filter">
176 <param name="var_obs" type="select" label="What to annotate?">
177 <option value="var">Variables (var)</option>
178 <option value="obs">Observations (obs)</option>
179 </param>
180 <conditional name="filter">
181 <param name="filter" type="select" label="Type of filtering?">
182 <option value="key">By key (column) values</option>
183 <option value="index">By index (row)</option>
184 </param>
185 <when value="key">
186 <param name="key" type="text" value="n_genes" label="Key to filter"/>
187 <conditional name="filter_key">
188 <param name="type" type="select" label="Type of value to filter">
189 <option value="number">Number</option>
190 <option value="text">Text</option>
191 <option value="boolean">Boolean</option>
192 </param>
193 <when value="number">
194 <param name="filter" type="select" label="Filter">
195 <option value="equal">equal to</option>
196 <option value="not_equal">not equal to</option>
197 <option value="less">less than</option>
198 <option value="less_or_equal">less than or equal to</option>
199 <option value="greater">greater than</option>
200 <option value="greater_or_equal">greater than or equal to</option>
201 </param>
202 <param name="value" type="float" value="2500" label="Value"/>
203 </when>
204 <when value="text">
205 <param name="filter" type="select" label="Filter">
206 <option value="equal">equal to</option>
207 <option value="not_equal">not equal to</option></param>
208 <param name="value" type="text" value="2500" label="Value"/>
209 </when>
210 <when value="boolean">
211 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/>
212 </when>
213 </conditional>
214 </when>
215 <when value="index">
216 <conditional name="index">
217 <param name="format" type="select" label="Format for the filter by index">
218 <option value="file">File</option>
219 <option value="text" selected="true">Text</option>
220 </param>
221 <when value="text">
222 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/>
223 </when>
224 <when value="file">
225 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/>
226 </when>
227 </conditional>
228 </when>
229 </conditional>
230 </when>
100 </conditional> 231 </conditional>
101 </inputs> 232 </inputs>
102 <outputs> 233 <outputs>
103 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}"/> 234 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}"/>
104 </outputs> 235 </outputs>
105 <tests> 236 <tests>
106 <test> 237 <test>
238 <!-- test 1 -->
107 <param name="input" value="krumsiek11.h5ad"/> 239 <param name="input" value="krumsiek11.h5ad"/>
108 <conditional name="manipulate"> 240 <conditional name="manipulate">
109 <param name="function" value="concatenate"/> 241 <param name="function" value="concatenate"/>
110 <param name="other_adatas" value="import.csv.h5ad"/> 242 <param name="other_adatas" value="import.csv.h5ad"/>
111 <param name="join" value="inner"/> 243 <param name="join" value="inner"/>
120 <has_text_matching expression="batch_key='batch'"/> 252 <has_text_matching expression="batch_key='batch'"/>
121 </assert_stdout> 253 </assert_stdout>
122 <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/> 254 <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/>
123 </test> 255 </test>
124 <test> 256 <test>
257 <!-- test 2 -->
125 <param name="input" value="krumsiek11.h5ad"/> 258 <param name="input" value="krumsiek11.h5ad"/>
126 <conditional name="manipulate"> 259 <conditional name="manipulate">
127 <param name="function" value="obs_names_make_unique"/> 260 <param name="function" value="obs_names_make_unique"/>
128 <param name="join" value="-"/> 261 <param name="join" value="-"/>
129 </conditional> 262 </conditional>
131 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/> 264 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
132 </assert_stdout> 265 </assert_stdout>
133 <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/> 266 <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
134 </test> 267 </test>
135 <test> 268 <test>
269 <!-- test 3 -->
136 <param name="input" value="krumsiek11.h5ad"/> 270 <param name="input" value="krumsiek11.h5ad"/>
137 <conditional name="manipulate"> 271 <conditional name="manipulate">
138 <param name="function" value="var_names_make_unique"/> 272 <param name="function" value="var_names_make_unique"/>
139 <param name="join" value="-"/> 273 <param name="join" value="-"/>
140 </conditional> 274 </conditional>
142 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/> 276 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
143 </assert_stdout> 277 </assert_stdout>
144 <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/> 278 <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
145 </test> 279 </test>
146 <test> 280 <test>
281 <!-- test 4 -->
147 <param name="input" value="krumsiek11.h5ad"/> 282 <param name="input" value="krumsiek11.h5ad"/>
148 <conditional name="manipulate"> 283 <conditional name="manipulate">
149 <param name="function" value="rename_categories"/> 284 <param name="function" value="rename_categories"/>
150 <param name="key" value="cell_type"/> 285 <param name="key" value="cell_type"/>
151 <param name="categories" value="Er,Ml,Mt, Ne, pr"/> 286 <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
156 <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/> 291 <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
157 </assert_stdout> 292 </assert_stdout>
158 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/> 293 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
159 </test> 294 </test>
160 <test> 295 <test>
296 <!-- test 5 -->
161 <param name="input" value="krumsiek11.h5ad"/> 297 <param name="input" value="krumsiek11.h5ad"/>
162 <conditional name="manipulate"> 298 <conditional name="manipulate">
163 <param name="function" value="strings_to_categoricals"/> 299 <param name="function" value="strings_to_categoricals"/>
164 </conditional> 300 </conditional>
165 <assert_stdout> 301 <assert_stdout>
166 <has_text_matching expression="adata.strings_to_categoricals"/> 302 <has_text_matching expression="adata.strings_to_categoricals"/>
167 </assert_stdout> 303 </assert_stdout>
168 <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/> 304 <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>
169 </test> 305 </test>
170 <test> 306 <test>
307 <!-- test 6 -->
171 <param name="input" value="krumsiek11.h5ad"/> 308 <param name="input" value="krumsiek11.h5ad"/>
172 <conditional name="manipulate"> 309 <conditional name="manipulate">
173 <param name="function" value="transpose"/> 310 <param name="function" value="transpose"/>
174 </conditional> 311 </conditional>
175 <assert_stdout> 312 <assert_stdout>
176 <has_text_matching expression="adata.transpose"/> 313 <has_text_matching expression="adata.transpose"/>
177 </assert_stdout> 314 </assert_stdout>
178 <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/> 315 <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>
316 </test>
317 <test>
318 <!-- test 7 -->
319 <param name="input" value="krumsiek11.h5ad"/>
320 <conditional name="manipulate">
321 <param name="function" value="add_annotation"/>
322 <param name="var_obs" value="var"/>
323 <param name="new_annot" value="var_add_annotation.tabular"/>
324 </conditional>
325 <output name="anndata" value="manipulate.add_annotation_var.h5ad" ftype="h5ad" compare="sim_size"/>
326 </test>
327 <test>
328 <!-- test 8 -->
329 <param name="input" value="krumsiek11.h5ad"/>
330 <conditional name="manipulate">
331 <param name="function" value="add_annotation"/>
332 <param name="var_obs" value="obs"/>
333 <param name="new_annot" value="obs_add_annotation.tabular"/>
334 </conditional>
335 <output name="anndata" value="manipulate.add_annotation_obs.h5ad" ftype="h5ad" compare="sim_size"/>
336 </test>
337 <test>
338 <!-- test 9 -->
339 <param name="input" value="krumsiek11.h5ad"/>
340 <conditional name="manipulate">
341 <param name="function" value="filter"/>
342 <param name="var_obs" value="var"/>
343 <conditional name="filter">
344 <param name="filter" value="index"/>
345 <conditional name="index">
346 <param name="format" value="text"/>
347 <param name="text" value="Gata2,EKLF"/>
348 </conditional>
349 </conditional>
350 </conditional>
351 <output name="anndata" value="manipulate.filter_var_index.h5ad" ftype="h5ad" compare="sim_size"/>
352 </test>
353 <test>
354 <!-- test 10 -->
355 <param name="input" value="krumsiek11.h5ad"/>
356 <conditional name="manipulate">
357 <param name="function" value="filter"/>
358 <param name="var_obs" value="obs"/>
359 <conditional name="filter">
360 <param name="filter" value="key"/>
361 <param name="key" value="cell_type"/>
362 <conditional name="filter_key">
363 <param name="type" value="text"/>
364 <param name="filter" value="equal"/>
365 <param name="value" value="progenitor"/>
366 </conditional>
367 </conditional>
368 </conditional>
369 <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
179 </test> 370 </test>
180 </tests> 371 </tests>
181 <help><![CDATA[ 372 <help><![CDATA[
182 **What it does** 373 **What it does**
183 374
208 Only affects string annotations that lead to less categories than the total number of observations. 399 Only affects string annotations that lead to less categories than the total number of observations.
209 400
210 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__) 401 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__)
211 402
212 Data matrix is transposed, observations and variables are interchanged. 403 Data matrix is transposed, observations and variables are interchanged.
404
405 - Add annotation for variables or observations
406
407 - Filter data variables or observations, by index or key
213 408
214 @HELP@ 409 @HELP@
215 ]]></help> 410 ]]></help>
216 <expand macro="citations"/> 411 <expand macro="citations"/>
217 </tool> 412 </tool>