scanpy_cluster_reduce_dimension: cluster_reduce

annotate cluster_reduce_dimension.xml @ 1:20cfb9f3dded draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"

author	iuc
date	Wed, 16 Oct 2019 06:29:43 -0400
parents	0e212e42ef88
children	dc2de14881ba

rev	line source
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster," version="@galaxy_version@">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2 <description>infer trajectories and embed with scanpy</description>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	3 <macros>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	4 <import>macros.xml</import>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	5 <xml name="pca_inputs">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	7 <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	8 <conditional name="pca">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	9 <param argument="chunked" type="select" label="Type of PCA?">
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	10 <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of `random_seed` and `svd_solver`)</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	11 <option value="False" selected="true">Full PCA</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	12 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	13 <when value="True">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	14 <param argument="chunk_size" type="integer" min="0" value="" label="chunk_size" help="Number of observations to include in each chunk"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	15 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	16 <when value="False">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	17 <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	18 label="Compute standard PCA from covariance matrix?"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	19 help="If not, it omits zero-centering variables (uses TruncatedSVD from scikit-learn), which allows to handle sparse input efficiently."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	20 <expand macro="svd_solver"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	21 <param argument="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	22 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	23 </conditional>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	24 <param argument="use_highly_variable" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use highly variable genes only?" help="They should be use if they have been determined beforehand."/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	25 </xml>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	26 <xml name="param_random_state">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	27 <param argument="random_state" type="integer" value="0" label="Random state" help="Change the initialization of the optimization."/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	28 </xml>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	29 <xml name="param_use_weights">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	30 <param argument="use_weights" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use weights from knn graph?"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	31 </xml>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	32 <token name="@CMD_pca_help@"><![CDATA[
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	33 The PCA is computed using the implementation of scikit-learn.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	34
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	35 The returned AnnData object contains:
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	36
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	37 - PCA coordinates in the multi-dimensional observation annotation (obsm)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	38 - Principal components containing the loadings in the multi-dimensional variable annotation (varm)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	39 - The variance decomposition in the unstructured annotation (uns)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	40 - Ratio of explained variance for PCA (variance)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	41 - Explained variance, equivalent to the eigenvalues of the covariance matrix
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	42
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	43 This data is accessible using the inspect tool for AnnData
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	44 ]]></token>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	45 <token name="@CMD_pca_params@"><![CDATA[
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	46 data=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	47 n_comps=$method.n_comps,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	48 dtype='$method.dtype',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	49 copy=False,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	50 chunked=$method.pca.chunked,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	51 #if $method.pca.chunked == 'True'
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	52 chunk_size=$method.pca.chunk_size,
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	53 #else
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	54 zero_center=$method.pca.zero_center,
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	55 svd_solver='$method.pca.svd_solver',
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	56 random_state=$method.pca.random_state,
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	57 #end if
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	58 use_highly_variable=$method.use_highly_variable
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	59 ]]></token>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	60 </macros>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	61 <expand macro="requirements"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	62 <expand macro="version_command"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	63 <command detect_errors="exit_code"><![CDATA[
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	64 @CMD@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	65 ]]></command>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	66 <configfiles>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	67 <configfile name="script_file"><![CDATA[
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	68 @CMD_imports@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	69 @CMD_read_inputs@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	70
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	71 #if $method.method == 'tl.louvain'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	72 sc.tl.louvain(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	73 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	74 flavor = '$method.flavor.flavor',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	75 #if $method.flavor.flavor == 'vtraag' and $method.flavor.resolution
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	76 resolution=$method.flavor.resolution,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	77 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	78 random_state=$method.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	79 key_added='$method.key_added',
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	80 directed=$method.directed,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	81 use_weights=$method.use_weights,
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	82 copy=False)
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	83
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	84 #else if $method.method == 'tl.leiden'
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	85 sc.tl.leiden(
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	86 adata=adata,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	87 resolution=$method.resolution,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	88 random_state=$method.random_state,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	89 key_added='$method.key_added',
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	90 use_weights=$method.use_weights,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	91 n_iterations=$method.n_iterations,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	92 copy=False)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	93
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	94 #else if $method.method == 'pp.pca'
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	95 sc.pp.pca(@CMD_pca_params@)
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	96
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	97 #else if $method.method == 'tl.pca'
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	98 sc.tl.pca(@CMD_pca_params@)
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	99
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	100 #else if $method.method == 'tl.diffmap'
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	101 sc.tl.diffmap(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	102 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	103 n_comps=$method.n_comps,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	104 copy =False)
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	105
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	106 #else if $method.method == 'tl.tsne'
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	107 sc.tl.tsne(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	108 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	109 #if $method.n_pcs
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	110 n_pcs=$method.n_pcs,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	111 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	112 perplexity=$method.perplexity,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	113 early_exaggeration=$method.early_exaggeration,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	114 learning_rate=$method.learning_rate,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	115 random_state=$method.random_state,
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	116 use_fast_tsne=$method.use_fast_tsne,
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	117 copy=False)
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	118
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	119 #else if $method.method == 'tl.umap'
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	120 sc.tl.umap(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	121 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	122 min_dist=$method.min_dist,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	123 spread=$method.spread,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	124 n_components=$method.n_components,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	125 #if $method.maxiter
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	126 maxiter=$method.maxiter,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	127 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	128 alpha=$method.alpha,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	129 gamma=$method.gamma,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	130 negative_sample_rate=$method.negative_sample_rate,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	131 init_pos='$method.init_pos',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	132 random_state=$method.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	133 copy=False)
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	134
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	135 #else if $method.method == 'tl.draw_graph'
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	136
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	137 #if str($method.adjacency) != 'None'
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	138 from scipy import io
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	139 adjacency = io.mmread('$method.adjacency')
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	140 #end if
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	141
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	142 sc.tl.draw_graph(
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	143 adata=adata,
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	144 layout='$method.layout',
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	145 #if str($method.root) != ''
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	146 #set $root=([int(x.strip()) for x in str($method.root).split(',')])
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	147 root=$root,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	148 #end if
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	149 random_state=$method.random_state,
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	150 #if str($method.init_pos) != ''
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	151 init_pos='$method.init_pos',
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	152 #end if
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	153 #if str($method.adjacency) != 'None'
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	154 adjacency=adjacency,
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	155 #end if
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	156 #if str($method.key_ext) != ''
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	157 key_ext='$method.key_ext',
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	158 #end if
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	159 copy=False)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	160
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	161 #else if $method.method == "tl.paga"
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	162 sc.tl.paga(
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	163 adata=adata,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	164 groups='$method.groups',
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	165 use_rna_velocity=$method.use_rna_velocity,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	166 model='$method.model',
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	167 copy=False)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	168
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	169 #else if $method.method == "tl.dpt"
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	170 sc.tl.dpt(
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	171 adata=adata,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	172 n_dcs=$method.n_dcs,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	173 n_branchings=$method.n_branchings,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	174 min_group_size=$method.min_group_size,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	175 allow_kendall_tau_shift=$method.allow_kendall_tau_shift,
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	176 copy=False)
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	177 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	178
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	179 @CMD_anndata_write_outputs@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	180 ]]></configfile>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	181 </configfiles>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	182 <inputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	183 <expand macro="inputs_anndata"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	184 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	185 <param argument="method" type="select" label="Method used for plotting">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	186 <option value="tl.louvain">Cluster cells into subgroups, using `tl.louvain`</option>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	187 <option value="tl.leiden">Cluster cells into subgroups, using `tl.leiden`</option>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	188 <option value="pp.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	189 <option value="tl.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	190 <option value="tl.diffmap">Diffusion Maps, using `tl.diffmap`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	191 <option value="tl.tsne">t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	192 <option value="tl.umap">Embed the neighborhood graph using UMAP, using `tl.umap`</option>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	193 <option value="tl.draw_graph">Force-directed graph drawing, using `tl.draw_graph`</option>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	194 <option value="tl.dpt">Infer progression of cells through geodesic distance along the graph, using `tl.dpt`</option>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	195 <option value="tl.paga">Generate cellular maps of differentiation manifolds with complex topologies, using `tl.paga`</option>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	196 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	197 <when value="tl.louvain">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	198 <conditional name="flavor">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	199 <param argument="flavor" type="select" label="Flavor for the clustering" help="">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	200 <option value="vtraag">vtraag (much more powerful)</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	201 <option value="igraph">igraph</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	202 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	203 <when value="vtraag">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	204 <param argument="resolution" type="float" value="" optional="true"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	205 label="Resolution"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	206 help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2009"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	207 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	208 <when value="igraph"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	209 </conditional>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	210 <expand macro="param_random_state"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	211 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help=""/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	212 <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	213 <expand macro="param_use_weights"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	214 </when>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	215 <when value="tl.leiden">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	216 <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	217 <expand macro="param_random_state"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	218 <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help=""/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	219 <expand macro="param_use_weights"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	220 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform." help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	221 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	222 <when value="pp.pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	223 <expand macro="pca_inputs"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	224 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	225 <when value="tl.pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	226 <expand macro="pca_inputs"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	227 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	228 <when value="tl.diffmap">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	229 <param argument="n_comps" type="integer" min="0" value="15" optional="true" label="Number of dimensions of the representation" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	230 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	231 <when value="tl.tsne">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	232 <param name="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	233 <param name="perplexity" type="float" value="30" label="Perplexity" help="The perplexity is related to the number of nearest neighbors that is used in other manifold learning algorithms. Larger datasets usually require a larger perplexity. Consider selecting a value between 5 and 50. The choice is not extremely critical since t-SNE is quite insensitive to this parameter."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	234 <param name="early_exaggeration" type="float" value="12.0" label="Early exaggeration" help="Controls how tight natural clusters in the original space are in the embedded space and how much space will be between them. For larger values, the space between natural clusters will be larger in the embedded space. Again, the choice of this parameter is not very critical. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	235 <param name="learning_rate" type="float" value="1000" label="Learning rate" help="The learning rate can be a critical parameter. It should be between 100 and 1000. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high. If the cost function gets stuck in a bad local minimum increasing the learning rate helps sometimes."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	236 <param name="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	237 <param argument="use_fast_tsne" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use the MulticoreTSNE package if possible?"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	238 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	239 <when value="tl.umap">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	240 <param argument="min_dist" type="float" value="0.5" label="Effective minimum distance between embedded points" help="Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the `spread` value, which determines the scale at which embedded points will be spread out. The default of in the `umap-learn` package is 0.1."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	241 <param argument="spread" type="float" value="1.0" label="Effective scale of embedded points" help="In combination with `min_dist` this determines how clustered/clumped the embedded points are."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	242 <param argument="n_components" type="integer" min="0" value="2" label="Number of dimensions of the embedding" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	243 <param argument="maxiter" type="integer" min="0" value="" optional="true" label="Number of iterations (epochs) of the optimization" help="Called `n_epochs` in the original UMAP."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	244 <param argument="alpha" type="float" value="1.0" label="Initial learning rate for the embedding optimization" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	245 <param argument="gamma" type="float" value="1.0" label="Weighting applied to negative samples in low dimensional embedding optimization" help="Values higher than one will result in greater weight being given to negative samples."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	246 <param argument="negative_sample_rate" type="integer" min="0" value="5" label="The number of negative edge/1-simplex samples to use per positive edge/1-simplex sample in optimizing the low dimensional embedding" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	247 <param argument="init_pos" type="select" label="How to initialize the low dimensional embedding" help="Called `init` in the original UMAP">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	248 <option value="paga">Position from paga</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	249 <option value="spectral" selected="true">Spectral embedding of the graph</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	250 <option value="random">Initial embedding positions at random</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	251 </param>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	252 <expand macro="param_random_state"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	253 </when>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	254 <when value="tl.draw_graph">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	255 <expand macro="param_layout"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	256 <expand macro="param_root"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	257 <expand macro="param_random_state"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	258 <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	259 <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	260 <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends `layout`"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	261 </when>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	262 <when value="tl.dpt">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	263 <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use" help=""/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	264 <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect" help=""/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	265 <param argument="min_group_size" type="float" min="0" value="0.01" label="Min group size" help="During recursive splitting of branches ('dpt groups') for `n_branchings` > 1, do not consider groups that contain less than `min_group_size` data points. If a float, `min_group_size` refers to a fraction of the total number of data points."/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	266 <param argument="allow_kendall_tau_shift" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Allow Kendal tau shift?" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of Haghverdi et al (2016) to stabilize the splitting."/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	267 </when>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	268 <when value="tl.paga">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	269 <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations (`adata.obs`)."/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	270 <param argument="use_rna_velocity" type="boolean" truevalue="False" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that `adata.uns` contains a directed single-cell graph with key `['velocyto_transitions']`. This feature might be subject to change in the future."/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	271 <param argument="model" type="select" label="PAGA connectivity model" help="">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	272 <option value="v1.2">v1.2</option>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	273 <option value="v1.0">v1.0</option>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	274 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	275 </when>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	276 </conditional>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	277 </inputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	278 <outputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	279 <expand macro="anndata_outputs"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	280 </outputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	281 <tests>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	282 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	283 <!-- test 1 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	284 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	285 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	286 <param name="method" value="tl.louvain"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	287 <conditional name="flavor">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	288 <param name="flavor" value="vtraag"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	289 <param name="resolution" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	290 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	291 <param name="random_state" value="10"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	292 <param name="key_added" value="louvain"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	293 <param name="directed" value="true"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	294 <param name="use_weights" value="false"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	295 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	296 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	297 <has_text_matching expression="sc.tl.louvain"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	298 <has_text_matching expression="adata=adata"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	299 <has_text_matching expression="flavor = 'vtraag'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	300 <has_text_matching expression="resolution=1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	301 <has_text_matching expression="random_state=10"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	302 <has_text_matching expression="key_added='louvain'"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	303 <has_text_matching expression="directed=True"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	304 <has_text_matching expression="use_weights=False"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	305 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	306 <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	307 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	308 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	309 <!-- test 2 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	310 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	311 <conditional name="method">
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	312 <param name="method" value="tl.leiden"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	313 <param name="random_state" value="1"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	314 <param name="random_state" value="10"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	315 <param name="key_added" value="leiden"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	316 <param name="use_weights" value="false"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	317 <param name="n_iterations" value="-1"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	318 </conditional>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	319 <assert_stdout>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	320 <has_text_matching expression="sc.tl.leiden"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	321 <has_text_matching expression="resolution=1"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	322 <has_text_matching expression="random_state=10"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	323 <has_text_matching expression="key_added='leiden'"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	324 <has_text_matching expression="use_weights=False"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	325 <has_text_matching expression="n_iterations=-1"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	326 </assert_stdout>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	327 <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	328 </test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	329 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	330 <!-- test 2 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	331 <param name="adata" value="krumsiek11.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	332 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	333 <param name="method" value="pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	334 <param name="n_comps" value="50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	335 <param name="dtype" value="float32"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	336 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	337 <param name="chunked" value="False"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	338 <param name="zero_center" value="true"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	339 <param name="svd_solver" value="auto"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	340 <param name="random_state" value="0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	341 </conditional>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	342 <param name="use_highly_variable" value="false"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	343 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	344 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	345 <has_text_matching expression="sc.pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	346 <has_text_matching expression="n_comps=50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	347 <has_text_matching expression="dtype='float32'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	348 <has_text_matching expression="copy=False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	349 <has_text_matching expression="chunked=False"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	350 <has_text_matching expression="zero_center=True"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	351 <has_text_matching expression="svd_solver='auto'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	352 <has_text_matching expression="random_state=0"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	353 <has_text_matching expression="use_highly_variable=False"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	354 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	355 <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	356 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	357 <!--<test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	358 < test 3 >
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	359 <param name="adata" value="krumsiek11.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	360 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	361 <param name="method" value="pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	362 <param name="n_comps" value="20"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	363 <param name="dtype" value="float32"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	364 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	365 <param name="chunked" value="True"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	366 <param name="chunk_size" value="50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	367 </conditional>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	368 <param name="use_highly_variable" value="false"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	369 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	370 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	371 <has_text_matching expression="sc.pp.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	372 <has_text_matching expression="data=adata"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	373 <has_text_matching expression="n_comps=20"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	374 <has_text_matching expression="dtype='float32'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	375 <has_text_matching expression="copy=False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	376 <has_text_matching expression="chunked=True"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	377 <has_text_matching expression="chunk_size=50"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	378 <has_text_matching expression="use_highly_variable=False"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	379 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	380 <output name="anndata_out" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	381 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	382 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	383 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	384 <!-- test 3 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	385 <param name="adata" value="krumsiek11.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	386 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	387 <param name="method" value="tl.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	388 <param name="n_comps" value="50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	389 <param name="dtype" value="float32"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	390 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	391 <param name="chunked" value="False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	392 <param name="zero_center" value="True"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	393 <param name="svd_solver" value="auto"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	394 <param name="random_state" value="0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	395 </conditional>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	396 <param name="use_highly_variable" value="false"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	397 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	398 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	399 <has_text_matching expression="sc.tl.pca"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	400 <has_text_matching expression="n_comps=50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	401 <has_text_matching expression="dtype='float32'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	402 <has_text_matching expression="copy=False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	403 <has_text_matching expression="chunked=False"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	404 <has_text_matching expression="zero_center=True"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	405 <has_text_matching expression="svd_solver='auto'"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	406 <has_text_matching expression="use_highly_variable=False"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	407 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	408 <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	409 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	410 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	411 <!-- test 4 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	412 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	413 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	414 <param name="method" value="tl.diffmap"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	415 <param name="n_comps" value="15"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	416 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	417 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	418 <has_text_matching expression="sc.tl.diffmap"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	419 <has_text_matching expression="n_comps=15"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	420 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	421 <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	422 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	423 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	424 <!-- test 5 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	425 <param name="adata" value="krumsiek11.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	426 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	427 <param name="method" value="tl.tsne"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	428 <param name="n_pcs" value="10"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	429 <param name="perplexity" value="30"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	430 <param name="early_exaggeration" value="12.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	431 <param name="learning_rate" value="1000"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	432 <param name="random_state" value="0"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	433 <param name="use_fast_tsne" value="true"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	434 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	435 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	436 <has_text_matching expression="sc.tl.tsne"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	437 <has_text_matching expression="n_pcs=10"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	438 <has_text_matching expression="perplexity=30.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	439 <has_text_matching expression="early_exaggeration=12.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	440 <has_text_matching expression="learning_rate=1000.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	441 <has_text_matching expression="random_state=0"/>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	442 <has_text_matching expression="use_fast_tsne=True"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	443 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	444 <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	445 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	446 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	447 <!-- test 6 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	448 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	449 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	450 <param name="method" value="tl.umap"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	451 <param name="min_dist" value="0.5"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	452 <param name="spread" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	453 <param name="n_components" value="2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	454 <param name="maxiter" value="2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	455 <param name="alpha" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	456 <param name="gamma" value="1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	457 <param name="negative_sample_rate" value="5"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	458 <param name="init_pos" value="spectral"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	459 <param name="random_state" value="0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	460 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	461 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	462 <has_text_matching expression="sc.tl.umap"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	463 <has_text_matching expression="min_dist=0.5"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	464 <has_text_matching expression="spread=1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	465 <has_text_matching expression="n_components=2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	466 <has_text_matching expression="maxiter=2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	467 <has_text_matching expression="alpha=1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	468 <has_text_matching expression="gamma=1.0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	469 <has_text_matching expression="negative_sample_rate=5"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	470 <has_text_matching expression="init_pos='spectral'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	471 <has_text_matching expression="random_state=0"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	472 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	473 <output name="anndata_out" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	474 <assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	475 <has_h5_keys keys="X, obs, obsm, uns, var" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	476 </assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	477 </output>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	478 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	479 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	480 <!-- test 7 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	481 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	482 <conditional name="method">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	483 <param name="method" value="tl.draw_graph"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	484 <param name="layout" value="fa"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	485 <param name="random_state" value="0"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	486 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	487 <assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	488 <has_text_matching expression="sc.tl.draw_graph"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	489 <has_text_matching expression="layout='fa'"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	490 <has_text_matching expression="random_state=0"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	491 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	492 <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	493 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	494 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	495 <!-- test 8 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	496 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	497 <conditional name="method">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	498 <param name="method" value="tl.paga"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	499 <param name="groups" value="paul15_clusters"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	500 <param name="use_rna_velocity" value="False"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	501 <param name="model" value="v1.2"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	502 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	503 <assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	504 <has_text_matching expression="sc.tl.paga"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	505 <has_text_matching expression="groups='paul15_clusters'"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	506 <has_text_matching expression="use_rna_velocity=False"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	507 <has_text_matching expression="model='v1.2'"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	508 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	509 <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	510 </test>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	511 <test>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	512 <!-- test 9 -->
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	513 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	514 <conditional name="method">
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	515 <param name="method" value="tl.dpt"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	516 <param name="n_dcs" value="15"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	517 <param name="n_branchings" value="1"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	518 <param name="min_group_size" value="0.01"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	519 <param name="allow_kendall_tau_shift" value="True"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	520 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	521 <assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	522 <has_text_matching expression="sc.tl.dpt"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	523 <has_text_matching expression="n_dcs=15"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	524 <has_text_matching expression="n_branchings=1"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	525 <has_text_matching expression="min_group_size=0.01"/>
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	526 <has_text_matching expression="allow_kendall_tau_shift=True"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	527 </assert_stdout>
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	528 <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	529 </test>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	530 </tests>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	531 <help><![CDATA[
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	532 Cluster cells into subgroups (`tl.louvain`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	533 ===========================================
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	534
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	535 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	536 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	537 analysis by Levine et al, 2015.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	538
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	539 This requires to run `pp.neighbors`, first.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	540
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	541 More details on the `scanpy documentation
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	542 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.louvain.html>`_
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	543
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	544 Cluster cells into subgroups (`tl.leiden`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	545 ==========================================
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	546
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	547 Cluster cells using the Leiden algorithm (Traag et al, 2018), an improved version of the Louvain algorithm (Blondel et al, 2008).
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	548
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	549 The Louvain algorithm has been proposed for single-cell analysis by Levine et al, 2015.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	550
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	551 More details on the `scanpy documentation
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	552 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.leiden.html>`_
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	553
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	554 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	555 ============================================================================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	556
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	557 @CMD_pca_outputs@
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	558
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	559 More details on the `scanpy documentation
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	560 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.pca.html>`__
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	561
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	562 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	563 ============================================================================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	564
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	565 @CMD_pca_outputs@
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	566
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	567 More details on the `scanpy documentation
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	568 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.pca.html>`__
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	569
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	570 Diffusion Maps, using `tl.diffmap`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	571 ==================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	572
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	573 Diffusion maps (Coifman et al 2005) has been proposed for visualizing single-cell
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	574 data by Haghverdi et al (2015). The tool uses the adapted Gaussian kernel suggested
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	575 by Haghverdi et al (2016) in the implementation of Wolf et al (2017).
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	576
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	577 The width ("sigma") of the connectivity kernel is implicitly determined by
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	578 the number of neighbors used to compute the single-cell graph in
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	579 `pp.neighbors`. To reproduce the original implementation
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	580 using a Gaussian kernel, use `method=='gauss'` in
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	581 `pp.neighbors`. To use an exponential kernel, use the default
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	582 `method=='umap'`. Differences between these options shouldn't usually be
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	583 dramatic.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	584
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	585 The diffusion map representation of data are added to the return AnnData in the multi-dimensional
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	586 observations annotation (obsm). It is the right eigen basis of the transition matrix with eigenvectors
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	587 as colum. It can be accessed using the inspect tool for AnnData
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	588
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	589 More details on the `scanpy documentation
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	590 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.diffmap.html>`__
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	591
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	592 t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	593 =======================================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	594
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	595 t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	596 proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	597 we use the implementation of scikit-learn (Pedregosa et al, 2011).
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	598
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	599 It returns `X_tsne`, tSNE coordinates of data.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	600
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	601 More details on the `scanpy documentation
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	602 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.tsne.html>`__
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	603
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	604 Embed the neighborhood graph using UMAP, using `tl.umap`
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	605 ========================================================
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	606
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	607 UMAP (Uniform Manifold Approximation and Projection) is a manifold learning
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	608 technique suitable for visualizing high-dimensional data. Besides tending to
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	609 be faster than tSNE, it optimizes the embedding such that it best reflects
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	610 the topology of the data, which we represent throughout Scanpy using a
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	611 neighborhood graph. tSNE, by contrast, optimizes the distribution of
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	612 nearest-neighbor distances in the embedding such that these best match the
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	613 distribution of distances in the high-dimensional space. We use the
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	614 implementation of `umap-learn <https://github.com/lmcinnes/umap>`__
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	615 (McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	616 <https://doi.org/10.1101/298430>`__.
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	617
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	618 The UMAP coordinates of data are added to the return AnnData in the multi-dimensional
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	619 observations annotation (obsm). This data is accessible using the inspect tool for AnnData
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	620
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	621 More details on the `scanpy documentation
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	622 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.umap.html>`__
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	623
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	624 Force-directed graph drawing, using `tl.draw_graph`
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	625 ===================================================
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	626
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	627 Force-directed graph drawing describes a class of long-established algorithms for visualizing graphs.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	628 It has been suggested for visualizing single-cell data by Islam et al, 11.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	629 Many other layouts as implemented in igraph are available. Similar approaches have been used by
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	630 Zunder et al, 2015 or Weinreb et al, 2016.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	631
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	632 This is an alternative to tSNE that often preserves the topology of the data better.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	633 This requires to run `pp.neighbors`, first.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	634
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	635 The default layout (ForceAtlas2) uses the package fa2.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	636
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	637 The coordinates of graph layout are added to the return AnnData in the multi-dimensional
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	638 observations annotation (obsm). This data is accessible using the inspect tool for AnnData.
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	639
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	640 More details on the `scanpy documentation
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	641 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.draw_graph.html>`__
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	642
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	643 Infer progression of cells through geodesic distance along the graph (`tl.dpt`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	644 ===============================================================================
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	645
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	646 Reconstruct the progression of a biological process from snapshot
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	647 data. `Diffusion Pseudotime` has been introduced by Haghverdi et al (2016) and
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	648 implemented within Scanpy (Wolf et al, 2017). Here, we use a further developed
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	649 version, which is able to deal with disconnected graphs (Wolf et al, 2017) and can
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	650 be run in a `hierarchical` mode by setting the parameter
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	651 `n_branchings>1`. We recommend, however, to only use
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	652 `tl.dpt` for computing pseudotime (`n_branchings=0`) and
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	653 to detect branchings via `paga`. For pseudotime, you need
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	654 to annotate your data with a root cell.
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	655
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	656 This requires to run `pp.neighbors`, first. In order to
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	657 reproduce the original implementation of DPT, use `method=='gauss'` in
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	658 this. Using the default `method=='umap'` only leads to minor quantitative
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	659 differences, though.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	660
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	661
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	662 If `n_branchings==0`, no field `dpt_groups` will be written.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	663
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	664 - dpt_pseudotime : Array of dim (number of samples) that stores the pseudotime of each cell, that is, the DPT distance with respect to the root cell.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	665 - dpt_groups : Array of dim (number of samples) that stores the subgroup id ('0','1', ...) for each cell. The groups typically correspond to 'progenitor cells', 'undecided cells' or 'branches' of a process.
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	666
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	667 The tool is similar to the R package `destiny` of Angerer et al (2016).
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	668
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	669 More details on the `tl.dpt scanpy documentation
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	670 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.dpt.html>`_
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	671
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	672
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	673 Generate cellular maps of differentiation manifolds with complex topologies (`tl.paga`)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	674 =======================================================================================
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	675
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	676 By quantifying the connectivity of partitions (groups, clusters) of the
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	677 single-cell graph, partition-based graph abstraction (PAGA) generates a much
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	678 simpler abstracted graph (PAGA graph) of partitions, in which edge weights
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	679 represent confidence in the presence of connections. By tresholding this
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	680 confidence in `paga`, a much simpler representation of data
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	681 can be obtained.
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	682
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	683 The confidence can be interpreted as the ratio of the actual versus the
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	684 expected value of connetions under the null model of randomly connecting
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	685 partitions. We do not provide a p-value as this null model does not
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	686 precisely capture what one would consider "connected" in real data, hence it
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	687 strongly overestimates the expected value. See an extensive discussion of
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	688 this in Wolf et al (2017).
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	689
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	690 Together with a random walk-based distance measure, this generates a partial
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	691 coordinatization of data useful for exploring and explaining its variation.
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	692
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	693 The returned AnnData object contains:
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	694
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	695 - Full adjacency matrix of the abstracted graph, weights correspond to confidence in the connectivities of partition (connectivities)
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	696 - Adjacency matrix of the tree-like subgraph that best explains the topology (connectivities_tree)
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	697
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	698 These datasets are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	699
1 20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	700 More details on the `tl.paga scanpy documentation
20cfb9f3dded "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	701 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.paga.html>`_
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	702 ]]></help>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	703 <expand macro="citations"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	704 </tool>

Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

annotate cluster_reduce_dimension.xml @ 1:20cfb9f3dded draft