Mercurial > repos > iuc > scanpy_cluster_reduce_dimension
comparison cluster_reduce_dimension.xml @ 8:35bc2eb568ed draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 13:03:42 +0000 |
| parents | b2df381a6004 |
| children | aaa5da8e73a9 |
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| 7:b2df381a6004 | 8:35bc2eb568ed |
|---|---|
| 1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@"> | 1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@"> |
| 2 <description>with scanpy</description> | 2 <description>with scanpy</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <xml name="pca_inputs"> | 5 <xml name="pca_inputs"> |
| 6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/> | 6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/> |
| 7 <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""> | 7 <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""> |
| 8 <expand macro="sanitize_query" /> | 8 <expand macro="sanitize_query" /> |
| 9 </param> | 9 </param> |
| 10 <conditional name="pca"> | 10 <conditional name="pca"> |
| 11 <param argument="chunked" type="select" label="Type of PCA?"> | 11 <param argument="chunked" type="select" label="Type of PCA?"> |
| 44 | 44 |
| 45 This data is accessible using the inspect tool for AnnData | 45 This data is accessible using the inspect tool for AnnData |
| 46 ]]></token> | 46 ]]></token> |
| 47 <token name="@CMD_pca_params@"><![CDATA[ | 47 <token name="@CMD_pca_params@"><![CDATA[ |
| 48 data=adata, | 48 data=adata, |
| 49 n_comps=$method.n_comps, | 49 n_comps=min($method.n_comps, adata.n_vars), |
| 50 dtype='$method.dtype', | 50 dtype='$method.dtype', |
| 51 copy=False, | 51 copy=False, |
| 52 chunked=$method.pca.chunked, | 52 chunked=$method.pca.chunked, |
| 53 #if $method.pca.chunked == 'True' | 53 #if $method.pca.chunked == 'True' |
| 54 chunk_size=$method.pca.chunk_size, | 54 chunk_size=$method.pca.chunk_size, |
| 59 #end if | 59 #end if |
| 60 use_highly_variable=$method.use_highly_variable | 60 use_highly_variable=$method.use_highly_variable |
| 61 ]]></token> | 61 ]]></token> |
| 62 </macros> | 62 </macros> |
| 63 <expand macro="requirements"> | 63 <expand macro="requirements"> |
| 64 <requirement type="package" version="0.6.1">louvain</requirement> | 64 <requirement type="package" version="0.7.0">louvain</requirement> |
| 65 </expand> | 65 </expand> |
| 66 <expand macro="version_command"/> | 66 <expand macro="version_command"/> |
| 67 <command detect_errors="exit_code"><![CDATA[ | 67 <command detect_errors="exit_code"><![CDATA[ |
| 68 @CMD@ | 68 @CMD@ |
| 69 ]]></command> | 69 ]]></command> |
| 102 sc.tl.pca(@CMD_pca_params@) | 102 sc.tl.pca(@CMD_pca_params@) |
| 103 | 103 |
| 104 #else if $method.method == 'tl.diffmap' | 104 #else if $method.method == 'tl.diffmap' |
| 105 sc.tl.diffmap( | 105 sc.tl.diffmap( |
| 106 adata=adata, | 106 adata=adata, |
| 107 n_comps=$method.n_comps, | 107 n_comps=min($method.n_comps, adata.n_vars), |
| 108 copy =False) | 108 copy =False) |
| 109 | 109 |
| 110 #else if $method.method == 'tl.tsne' | 110 #else if $method.method == 'tl.tsne' |
| 111 sc.tl.tsne( | 111 sc.tl.tsne( |
| 112 adata=adata, | 112 adata=adata, |
| 370 <param name="show_log" value="true" /> | 370 <param name="show_log" value="true" /> |
| 371 </section> | 371 </section> |
| 372 <output name="hidden_output"> | 372 <output name="hidden_output"> |
| 373 <assert_contents> | 373 <assert_contents> |
| 374 <has_text_matching expression="sc.pp.pca"/> | 374 <has_text_matching expression="sc.pp.pca"/> |
| 375 <has_text_matching expression="n_comps=50"/> | |
| 376 <has_text_matching expression="dtype='float32'"/> | 375 <has_text_matching expression="dtype='float32'"/> |
| 377 <has_text_matching expression="copy=False"/> | 376 <has_text_matching expression="copy=False"/> |
| 378 <has_text_matching expression="chunked=False"/> | 377 <has_text_matching expression="chunked=False"/> |
| 379 <has_text_matching expression="zero_center=True"/> | 378 <has_text_matching expression="zero_center=True"/> |
| 380 <has_text_matching expression="svd_solver='auto'"/> | 379 <has_text_matching expression="svd_solver='auto'"/> |
| 381 <has_text_matching expression="random_state=0"/> | 380 <has_text_matching expression="random_state=0"/> |
| 382 <has_text_matching expression="use_highly_variable=False"/> | 381 <has_text_matching expression="use_highly_variable=False"/> |
| 383 </assert_contents> | 382 </assert_contents> |
| 384 </output> | 383 </output> |
| 385 <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> | 384 <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/> |
| 386 </test> | 385 </test> |
| 387 <!--<test> | 386 <!--<test> |
| 388 < test 3 > | 387 < test 3 > |
| 389 <param name="adata" value="krumsiek11.h5ad" /> | 388 <param name="adata" value="krumsiek11.h5ad" /> |
| 390 <conditional name="method"> | 389 <conditional name="method"> |
| 429 <param name="show_log" value="true" /> | 428 <param name="show_log" value="true" /> |
| 430 </section> | 429 </section> |
| 431 <output name="hidden_output"> | 430 <output name="hidden_output"> |
| 432 <assert_contents> | 431 <assert_contents> |
| 433 <has_text_matching expression="sc.tl.pca"/> | 432 <has_text_matching expression="sc.tl.pca"/> |
| 434 <has_text_matching expression="n_comps=50"/> | |
| 435 <has_text_matching expression="dtype='float32'"/> | 433 <has_text_matching expression="dtype='float32'"/> |
| 436 <has_text_matching expression="copy=False"/> | 434 <has_text_matching expression="copy=False"/> |
| 437 <has_text_matching expression="chunked=False"/> | 435 <has_text_matching expression="chunked=False"/> |
| 438 <has_text_matching expression="zero_center=True"/> | 436 <has_text_matching expression="zero_center=True"/> |
| 439 <has_text_matching expression="svd_solver='auto'"/> | 437 <has_text_matching expression="svd_solver='auto'"/> |
| 440 <has_text_matching expression="use_highly_variable=False"/> | 438 <has_text_matching expression="use_highly_variable=False"/> |
| 441 </assert_contents> | 439 </assert_contents> |
| 442 </output> | 440 </output> |
| 443 <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> | 441 <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/> |
| 444 </test> | 442 </test> |
| 445 <test> | 443 <test> |
| 446 <!-- test 3 --> | 444 <!-- test 3 --> |
| 447 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> | 445 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> |
| 448 <conditional name="method"> | 446 <conditional name="method"> |
| 453 <param name="show_log" value="true" /> | 451 <param name="show_log" value="true" /> |
| 454 </section> | 452 </section> |
| 455 <output name="hidden_output"> | 453 <output name="hidden_output"> |
| 456 <assert_contents> | 454 <assert_contents> |
| 457 <has_text_matching expression="sc.tl.diffmap"/> | 455 <has_text_matching expression="sc.tl.diffmap"/> |
| 458 <has_text_matching expression="n_comps=15"/> | |
| 459 </assert_contents> | 456 </assert_contents> |
| 460 </output> | 457 </output> |
| 461 <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> | 458 <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> |
| 462 </test> | 459 </test> |
| 463 <test> | 460 <test> |