Mercurial > repos > iuc > anndata_manipulate

comparison manipulate.xml @ 12:ed4996a16f7f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
author iuc
date Sun, 12 Nov 2023 16:42:25 +0000
parents 3d748954434b
children
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11:3d748954434b 12:ed4996a16f7f
18 ]]></command> 18 ]]></command>
19 <configfiles> 19 <configfiles>
20 <configfile name="script_file"><![CDATA[ 20 <configfile name="script_file"><![CDATA[
21 @CMD_imports@ 21 @CMD_imports@
22 22
23 adata = ad.read('$input') 23 adata = ad.read_h5ad('$input')
24 24
25 #if $manipulate.function == 'concatenate' 25 #if $manipulate.function == 'concatenate'
26 #for i, filepath in enumerate($manipulate.other_adatas) 26 #for i, filepath in enumerate($manipulate.other_adatas)
27 adata_$i = ad.read('$filepath') 27 adata_$i = ad.read_h5ad('$filepath')
28 #end for 28 #end for
29 adata = adata.concatenate( 29 adata = adata.concatenate(
30 #for i, filepath in enumerate($manipulate.other_adatas) 30 #for i, filepath in enumerate($manipulate.other_adatas)
31 adata_$i, 31 adata_$i,
32 #end for 32 #end for
172 <when value="add_annotation"> 172 <when value="add_annotation">
173 <param name="var_obs" type="select" label="What to annotate?"> 173 <param name="var_obs" type="select" label="What to annotate?">
174 <option value="var">Variables (var)</option> 174 <option value="var">Variables (var)</option>
175 <option value="obs">Observations (obs)</option> 175 <option value="obs">Observations (obs)</option>
176 </param> 176 </param>
177 <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"
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)"/> 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)"/>
179 </when> 179 </when>
180 <when value="filter"> 180 <when value="filter">
181 <param name="var_obs" type="select" label="What to filter?"> 181 <param name="var_obs" type="select" label="What to filter?">
182 <option value="var">Variables (var)</option> 182 <option value="var">Variables (var)</option>
287 <!-- test 4 --> 287 <!-- test 4 -->
288 <param name="input" value="krumsiek11.h5ad"/> 288 <param name="input" value="krumsiek11.h5ad"/>
289 <conditional name="manipulate"> 289 <conditional name="manipulate">
290 <param name="function" value="rename_categories"/> 290 <param name="function" value="rename_categories"/>
291 <param name="key" value="cell_type"/> 291 <param name="key" value="cell_type"/>
292 <param name="categories" value="Er,Ml,Mt, Ne, pr"/> 292 <param name="categories" value="Ery, Mk, Mo, progenitor"/>
293 </conditional> 293 </conditional>
294 <assert_stdout> 294 <assert_stdout>
295 <has_text_matching expression="adata.rename_categories"/> 295 <has_text_matching expression="adata.rename_categories"/>
296 <has_text_matching expression="key='cell_type'"/> 296 <has_text_matching expression="key='cell_type'"/>
297 <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/> 297 <has_text_matching expression="categories=\['Ery', 'Mk', 'Mo', 'progenitor'\]"/>
298 </assert_stdout> 298 </assert_stdout>
299 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/> 299 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
300 </test> 300 </test>
301 <test> 301 <test>
302 <!-- test 5 --> 302 <!-- test 5 -->