Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

comparison cluster_reduce_dimension.xml @ 8:35bc2eb568ed draft

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"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
comparison
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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>