Mercurial > repos > iuc > anndata_manipulate

comparison manipulate.xml @ 2:a56baceb1900 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
author iuc
date Thu, 12 Dec 2019 09:22:35 -0500
parents 19592ec717ef
children d4af736e7b83
comparison
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1:19592ec717ef 2:a56baceb1900
118 #if $manipulate.var_obs == 'var' 118 #if $manipulate.var_obs == 'var'
119 adata = adata[:,filtered] 119 adata = adata[:,filtered]
120 #else if $manipulate.var_obs == 'obs' 120 #else if $manipulate.var_obs == 'obs'
121 adata = adata[filtered, :] 121 adata = adata[filtered, :]
122 #end if 122 #end if
123
124 #else if $manipulate.function == 'save_raw'
125 adata.raw = adata
126
123 #end if 127 #end if
124 128
125 adata.write('anndata.h5ad') 129 adata.write('anndata.h5ad')
126 ]]></configfile> 130 ]]></configfile>
127 </configfiles> 131 </configfiles>
135 <option value="rename_categories">Rename categories of annotation</option> 139 <option value="rename_categories">Rename categories of annotation</option>
136 <option value="strings_to_categoricals">Transform string annotations to categoricals</option> 140 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
137 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option> 141 <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> 142 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
139 <option value="filter">Filter observations or variables</option> 143 <option value="filter">Filter observations or variables</option>
144 <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
140 </param> 145 </param>
141 <when value="concatenate"> 146 <when value="concatenate">
142 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/> 147 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
143 <param name="join" type="select" label="Join method"> 148 <param name="join" type="select" label="Join method">
144 <option value="inner">Intersection of variables</option> 149 <option value="inner">Intersection of variables</option>
171 </param> 176 </param>
172 <param name="new_annot" type="data" format="tabular" label="Table with new annotations" 177 <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)"/> 178 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> 179 </when>
175 <when value="filter"> 180 <when value="filter">
176 <param name="var_obs" type="select" label="What to annotate?"> 181 <param name="var_obs" type="select" label="What to filter?">
177 <option value="var">Variables (var)</option> 182 <option value="var">Variables (var)</option>
178 <option value="obs">Observations (obs)</option> 183 <option value="obs">Observations (obs)</option>
179 </param> 184 </param>
180 <conditional name="filter"> 185 <conditional name="filter">
181 <param name="filter" type="select" label="Type of filtering?"> 186 <param name="filter" type="select" label="Type of filtering?">
366 </conditional> 371 </conditional>
367 </conditional> 372 </conditional>
368 </conditional> 373 </conditional>
369 <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/> 374 <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
370 </test> 375 </test>
376 <test>
377 <!-- test 11 -->
378 <param name="input" value="krumsiek11.h5ad"/>
379 <conditional name="manipulate">
380 <param name="function" value="save_raw"/>
381 </conditional>
382 <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size"/>
383 </test>
371 </tests> 384 </tests>
372 <help><![CDATA[ 385 <help><![CDATA[
373 **What it does** 386 **What it does**
374 387
375 This tool takes a AnnData dataset, manipulates it and returns it. 388 This tool takes a AnnData dataset, manipulates it and returns it.
403 Data matrix is transposed, observations and variables are interchanged. 416 Data matrix is transposed, observations and variables are interchanged.
404 417
405 - Add annotation for variables or observations 418 - Add annotation for variables or observations
406 419
407 - Filter data variables or observations, by index or key 420 - Filter data variables or observations, by index or key
421
422 - Freeze the current state into the 'raw' attribute
408 423
409 @HELP@ 424 @HELP@
410 ]]></help> 425 ]]></help>
411 <expand macro="citations"/> 426 <expand macro="citations"/>
412 </tool> 427 </tool>