Mercurial > repos > iuc > scanpy_normalize
comparison normalize.xml @ 11:c9cb76cf8d6c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
| author | iuc |
|---|---|
| date | Wed, 08 Nov 2023 14:49:18 +0000 |
| parents | ab55fe8030b6 |
| children | 94c19fb1281c |
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| 10:ab55fe8030b6 | 11:c9cb76cf8d6c |
|---|---|
| 1 <tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" profile="@profile@"> | 1 <tool id="scanpy_normalize" name="Normalize" version="@galaxy_version@" 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 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 10 @CMD@ | 10 @CMD@ |
| 11 ]]></command> | 11 ]]></command> |
| 124 </inputs> | 124 </inputs> |
| 125 <outputs> | 125 <outputs> |
| 126 <expand macro="anndata_outputs"/> | 126 <expand macro="anndata_outputs"/> |
| 127 </outputs> | 127 </outputs> |
| 128 <tests> | 128 <tests> |
| 129 <test> | 129 <test expect_num_outputs="2"> |
| 130 <!-- test 0 --> | 130 <!-- test 1 --> |
| 131 <param name="adata" value="krumsiek11.h5ad" /> | 131 <param name="adata" value="krumsiek11.h5ad" /> |
| 132 <conditional name="method"> | 132 <conditional name="method"> |
| 133 <param name="method" value="pp.normalize_total"/> | 133 <param name="method" value="pp.normalize_total"/> |
| 134 <conditional name="exclude_highly_expressed"> | 134 <conditional name="exclude_highly_expressed"> |
| 135 <param name="exclude_highly_expressed" value="False"/> | 135 <param name="exclude_highly_expressed" value="False"/> |
| 149 <has_text_matching expression="layers='all'"/> | 149 <has_text_matching expression="layers='all'"/> |
| 150 </assert_contents> | 150 </assert_contents> |
| 151 </output> | 151 </output> |
| 152 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> | 152 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> |
| 153 </test> | 153 </test> |
| 154 <test> | 154 <test expect_num_outputs="2"> |
| 155 <!-- test 1 --> | 155 <!-- test 2 --> |
| 156 <param name="adata" value="random-randint.h5ad"/> | 156 <param name="adata" value="random-randint.h5ad"/> |
| 157 <conditional name="method"> | 157 <conditional name="method"> |
| 158 <param name="method" value="pp.recipe_zheng17"/> | 158 <param name="method" value="pp.recipe_zheng17"/> |
| 159 <param name="n_top_genes" value="1000"/> | 159 <param name="n_top_genes" value="1000"/> |
| 160 <param name="log" value="True"/> | 160 <param name="log" value="True"/> |
| 169 <has_text_matching expression="log=True"/> | 169 <has_text_matching expression="log=True"/> |
| 170 </assert_contents> | 170 </assert_contents> |
| 171 </output> | 171 </output> |
| 172 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/> | 172 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size" delta="1000000" delta_frac="0.15"/> |
| 173 </test> | 173 </test> |
| 174 <test> | 174 <test expect_num_outputs="2"> |
| 175 <!-- test 2 --> | 175 <!-- test 3 --> |
| 176 <param name="adata" value="paul15_subsample.h5ad" /> | 176 <param name="adata" value="paul15_subsample.h5ad" /> |
| 177 <conditional name="method"> | 177 <conditional name="method"> |
| 178 <param name="method" value="pp.recipe_weinreb17"/> | 178 <param name="method" value="pp.recipe_weinreb17"/> |
| 179 <param name="log" value="True"/> | 179 <param name="log" value="True"/> |
| 180 <param name="mean_threshold" value="0.01"/> | 180 <param name="mean_threshold" value="0.01"/> |
| 197 <has_text_matching expression="random_state=0"/> | 197 <has_text_matching expression="random_state=0"/> |
| 198 </assert_contents> | 198 </assert_contents> |
| 199 </output> | 199 </output> |
| 200 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/> | 200 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/> |
| 201 </test> | 201 </test> |
| 202 <test> | 202 <test expect_num_outputs="2"> |
| 203 <!-- test 3 --> | 203 <!-- test 4 --> |
| 204 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" /> | 204 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" /> |
| 205 <conditional name="method"> | 205 <conditional name="method"> |
| 206 <param name="method" value="pp.recipe_seurat"/> | 206 <param name="method" value="pp.recipe_seurat"/> |
| 207 <param name="log" value="True"/> | 207 <param name="log" value="True"/> |
| 208 </conditional> | 208 </conditional> |
| 226 the same total count after normalization. | 226 the same total count after normalization. |
| 227 | 227 |
| 228 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. | 228 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. |
| 229 | 229 |
| 230 More details on the `scanpy documentation | 230 More details on the `scanpy documentation |
| 231 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.normalize_per_cell.html>`__ | 231 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__ |
| 232 | 232 |
| 233 | 233 |
| 234 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) | 234 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) |
| 235 ================================================================================================================== | 235 ================================================================================================================== |
| 236 | 236 |
| 245 - renormalize after filtering | 245 - renormalize after filtering |
| 246 - log transform (if needed) | 246 - log transform (if needed) |
| 247 - scale to unit variance and shift to zero mean | 247 - scale to unit variance and shift to zero mean |
| 248 | 248 |
| 249 More details on the `scanpy documentation | 249 More details on the `scanpy documentation |
| 250 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_zheng17.html>`__ | 250 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__ |
| 251 | 251 |
| 252 | 252 |
| 253 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) | 253 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) |
| 254 ============================================================================== | 254 ============================================================================== |
| 255 | 255 |
| 256 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. | 256 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. |
| 257 | 257 |
| 258 More details on the `scanpy documentation | 258 More details on the `scanpy documentation |
| 259 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_weinreb17.html>`__ | 259 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__ |
| 260 | 260 |
| 261 | 261 |
| 262 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) | 262 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) |
| 263 ========================================================================== | 263 ========================================================================== |
| 264 | 264 |
| 265 This uses a particular preprocessing. | 265 This uses a particular preprocessing. |
| 266 | 266 |
| 267 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. | 267 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. |
| 268 | 268 |
| 269 More details on the `scanpy documentation | 269 More details on the `scanpy documentation |
| 270 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_seurat.html>`__ | 270 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__ |
| 271 | 271 |
| 272 ]]></help> | 272 ]]></help> |
| 273 <expand macro="citations"/> | 273 <expand macro="citations"/> |
| 274 </tool> | 274 </tool> |