Mercurial > repos > iuc > scanpy_remove_confounders

comparison remove_confounders.xml @ 12:25ab7843ad7a 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 18:05:53 +0000
parents daa329d0ee55
children e078f7503d29
comparison
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11:0a1480457f9d 12:25ab7843ad7a
1 <tool id="scanpy_remove_confounders" name="Remove confounders" version="@galaxy_version@" profile="@profile@"> 1 <tool id="scanpy_remove_confounders" name="Remove confounders" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
2 <description>with scanpy</description> 2 <description>with scanpy</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @CMD@ 9 @CMD@
10 ]]></command> 10 ]]></command>
11 <configfiles> 11 <configfiles>
28 sc.pp.mnn_correct( 28 sc.pp.mnn_correct(
29 adata, 29 adata,
30 #for i, filepath in enumerate($methods.extra_adata) 30 #for i, filepath in enumerate($methods.extra_adata)
31 adata_$i, 31 adata_$i,
32 #end for 32 #end for
33 #if str($methods.var_subset) != '' 33 #if $methods.var_subset
34 #set $var_subset=([x.strip() for x in str($method.var_subset).split(',')]) 34 #set $var_subset=([x.strip() for x in str($method.var_subset).split(',')])
35 var_subset=$var_subset, 35 var_subset=$var_subset,
36 #end if 36 #end if
37 batch_key='$method.batch_key', 37 batch_key='$method.batch_key',
38 index_unique='$method.index_unique' 38 index_unique='$method.index_unique'
39 #if str($methods.batch_categories) != '' 39 #if $methods.batch_categories
40 #set $batch_categories=([x.strip() for x in str($method.batch_categories).split(',')]) 40 #set $batch_categories=([x.strip() for x in str($method.batch_categories).split(',')])
41 batch_categories=$batch_categories, 41 batch_categories=$batch_categories,
42 #end if 42 #end if
43 k=$method.k, 43 k=$method.k,
44 sigma=$method.sigma, 44 sigma=$method.sigma,
120 </inputs> 120 </inputs>
121 <outputs> 121 <outputs>
122 <expand macro="anndata_outputs"/> 122 <expand macro="anndata_outputs"/>
123 </outputs> 123 </outputs>
124 <tests> 124 <tests>
125 <test> 125 <test expect_num_outputs="2">
126 <!-- test 0 --> 126 <!-- test 0 -->
127 <param name="adata" value="krumsiek11.h5ad" /> 127 <param name="adata" value="krumsiek11.h5ad" />
128 <conditional name="method"> 128 <conditional name="method">
129 <param name="method" value="pp.regress_out"/> 129 <param name="method" value="pp.regress_out"/>
130 <param name="keys" value="cell_type"/> 130 <param name="keys" value="cell_type"/>
138 <has_text_matching expression="keys=\['cell_type'\]"/> 138 <has_text_matching expression="keys=\['cell_type'\]"/>
139 </assert_contents> 139 </assert_contents>
140 </output> 140 </output>
141 <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 141 <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
142 </test> 142 </test>
143 <!--<test> 143 <!--<test expect_num_outputs="2">
144 < test 2 > 144 < test 2 >
145 <param name="adata" value="krumsiek11.h5ad" /> 145 <param name="adata" value="krumsiek11.h5ad" />
146 <conditional name="method"> 146 <conditional name="method">
147 <param name="method" value="pp.mnn_correct"/> 147 <param name="method" value="pp.mnn_correct"/>
148 <param name="reg_keys" value="cell_type"/> 148 <param name="reg_keys" value="cell_type"/>
151 <has_text_matching expression="sc.pp.mnn_correct"/> 151 <has_text_matching expression="sc.pp.mnn_correct"/>
152 <has_text_matching expression="keys='cell_type'"/> 152 <has_text_matching expression="keys='cell_type'"/>
153 </assert_stdout> 153 </assert_stdout>
154 <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 154 <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
155 </test>--> 155 </test>-->
156 <test> 156 <test expect_num_outputs="2">
157 <!-- test 1 --> 157 <!-- test 1 -->
158 <param name="adata" value="blobs.h5ad" /> 158 <param name="adata" value="blobs.h5ad" />
159 <conditional name="method"> 159 <conditional name="method">
160 <param name="method" value="pp.combat"/> 160 <param name="method" value="pp.combat"/>
161 <param name="key" value="blobs"/> 161 <param name="key" value="blobs"/>
178 178
179 Regress out unwanted sources of variation, using simple linear regression. This is 179 Regress out unwanted sources of variation, using simple linear regression. This is
180 inspired by Seurat's `regressOut` function in R. 180 inspired by Seurat's `regressOut` function in R.
181 181
182 More details on the `scanpy documentation 182 More details on the `scanpy documentation
183 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.regress_out.html>`__ 183 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.regress_out.html>`__
184 184
185 Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct` 185 Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct`
186 ================================================================================== 186 ==================================================================================
187 187
188 This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the 188 This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the
189 original order containing corrected expression values or a concatenated matrix or AnnData object. 189 original order containing corrected expression values or a concatenated matrix or AnnData object.
190 190
191 Be reminded that it is not advised to use the corrected data matrices for differential expression testing. 191 Be reminded that it is not advised to use the corrected data matrices for differential expression testing.
192 192
193 More details on the `scanpy documentation 193 More details on the `scanpy documentation
194 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.api.pp.mnn_correct.html>`__ 194 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.mnn_correct.html>`__
195 195
196 196
197 Correct batch effects with ComBat function (`pp.combat`) 197 Correct batch effects with ComBat function (`pp.combat`)
198 ======================================================== 198 ========================================================
199 199
200 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat 200 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat
201 201
202 More details on the `scanpy documentation 202 More details on the `scanpy documentation
203 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.combat.html>`__ 203 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.combat.html>`__
204 204
205 205
206 ]]></help> 206 ]]></help>
207 <expand macro="citations"/> 207 <expand macro="citations"/>
208 </tool> 208 </tool>