scanpy_cluster_reduce_dimension: cluster_reduce

author	iuc
date	Mon, 04 Mar 2019 10:13:44 -0500
parents
children	20cfb9f3dded

rev	line source
0 0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster and reduce dimension with scanpy" version="@galaxy_version@">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2 <description></description>
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">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	6 <param name="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	7 <param name="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""/>
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">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	9 <param name="chunked" type="select" label="Type of PCA?">
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">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	14 <param name="chunk_size" type="integer" min="0" value="" label="chunk_size" help="Number of observations to include in each chunk"/>
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">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	17 <param name="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
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"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	21 <param name="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
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>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	24 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	25 <token name="@CMD_pca_outputs@"><![CDATA[
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	26 np.savetxt('$X_pca', adata.obsm['X_pca'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	27 np.savetxt('$PCs', adata.varm['PCs'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	28 np.savetxt('$variance', adata.uns['pca']['variance'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	29 np.savetxt('$variance_ratio', adata.uns['pca']['variance_ratio'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	30 ]]></token>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	31 <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	32 data=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	33 n_comps=$method.n_comps,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	34 dtype='$method.dtype',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	35 copy=False,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	36 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	37 #if $method.pca.chunked == 'True'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	38 chunk_size=$method.pca.chunk_size
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	39 #else
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	40 zero_center='$method.pca.zero_center',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	41 svd_solver='$method.pca.svd_solver',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	42 random_state=$method.pca.random_state
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	43 #end if
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 <xml name="penalty">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	46 <param argument="penalty" type="select" label="Norm used in the penalization" help="">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	47 <option value="l1">l1</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	48 <option value="l2">l2</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	49 <option value="customized">customized</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	50 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	51 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	52 <xml name="custom_penalty">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	53 <param argument="pen" type="text" value="" label="Norm used in the penalization" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	54 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	55 <xml name="fit_intercept">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	56 <param argument="fit_intercept" type="boolean" truevalue="True" falsevalue="False" checked="true"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	57 label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	58 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	59 <xml name="random_state">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	60 <param argument="random_state" type="integer" value="" optional="true"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	61 label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	62 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	63 <xml name="max_iter">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	64 <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	65 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	66 <xml name="multi_class">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	67 <param argument="multi_class" type="select" label="Multi class" help="">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	68 <option value="ovr">ovr: a binary problem is fit for each label</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	69 <option value="multinomial">multinomial: the multinomial loss fit across the entire probability distribution, even when the data is binary</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	70 <option value="auto">auto: selects ‘ovr’ if the data is binary and otherwise selects ‘multinomial’</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	71 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	72 </xml>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	73 </macros>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	74 <expand macro="requirements"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	75 <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	76 <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	77 @CMD@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	78 ]]></command>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	79 <configfiles>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	80 <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	81 @CMD_imports@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	82 @CMD_read_inputs@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	83
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	84 #if $method.method == 'tl.louvain'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	85 sc.tl.louvain(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	86 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	87 flavor = '$method.flavor.flavor',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	88 #if $method.flavor.flavor == 'vtraag' and $method.flavor.resolution
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	89 resolution=$method.flavor.resolution,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	90 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	91 random_state=$method.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	92 key_added='$method.key_added',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	93 copy=False)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	94 #elif $method.method == 'pp.pca'
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@)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	96 @CMD_pca_outputs@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	97 #elif $method.method == 'tl.pca'
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@)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	99 @CMD_pca_outputs@
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	100 #elif $method.method == 'tl.diffmap'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	101 sc.tl.diffmap(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	102 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	103 n_comps=$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)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	105 np.savetxt('$X_diffmap', adata.obsm['X_diffmap'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	106 #elif $method.method == 'tl.tsne'
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,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	116 copy=False)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	117 np.savetxt('$X_tsne', adata.obsm['X_tsne'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	118 #elif $method.method == 'tl.umap'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	119 sc.tl.umap(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	120 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	121 min_dist=$method.min_dist,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	122 spread=$method.spread,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	123 n_components=$method.n_components,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	124 #if $method.maxiter
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	125 maxiter=$method.maxiter,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	126 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	127 alpha=$method.alpha,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	128 gamma=$method.gamma,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	129 negative_sample_rate=$method.negative_sample_rate,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	130 init_pos='$method.init_pos',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	131 random_state=$method.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	132 copy=False)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	133 np.savetxt('$X_umap', adata.obsm['X_umap'], delimiter='\t')
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	134 #elif $method.method == 'pp.neighbors'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	135 sc.pp.neighbors(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	136 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	137 n_neighbors=$method.n_neighbors,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	138 #if $method.n_pcs
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	139 n_pcs=$method.n_pcs,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	140 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	141 knn=$method.knn,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	142 random_state=$method.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	143 method='$method.pp_neighbors_method',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	144 metric='$method.metric',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	145 copy=False)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	146 #elif $method.method == 'tl.rank_genes_groups'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	147 sc.tl.rank_genes_groups(
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	148 adata=adata,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	149 groupby='$method.groupby',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	150 use_raw=$method.use_raw,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	151 #if str($method.groups) != ''
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	152 groups='$method.groups',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	153 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	154 #if $method.ref.rest == 'rest'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	155 reference='$method.ref.rest',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	156 #else
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	157 reference='$method.ref.reference',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	158 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	159 n_genes=$method.n_genes,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	160 method='$method.tl_rank_genes_groups_method.method',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	161 #if $method.tl_rank_genes_groups_method.method == 'logreg'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	162 solver='$method.tl_rank_genes_groups_method.solver.solver',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	163 #if $method.tl_rank_genes_groups_method.solver.solver == 'newton-cg'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	164 penalty='l2',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	165 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	166 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	167 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	168 #else if $method.tl_rank_genes_groups_method.solver.solver == 'lbfgs'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	169 penalty='l2',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	170 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	171 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	172 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	173 #else if $method.tl_rank_genes_groups_method.solver.solver == 'liblinear'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	174 #if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l1'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	175 penalty='l1',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	176 #else if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l2'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	177 penalty='l2',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	178 dual=$method.tl_rank_genes_groups_method.solver.penalty.dual,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	179 #else
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	180 penalty='$method.tl_rank_genes_groups_method.solver.penalty.pen',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	181 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	182 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	183 #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	184 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	185 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	186 #if $method.tl_rank_genes_groups_method.solver.random_state
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	187 random_state=$method.tl_rank_genes_groups_method.solver.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	188 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	189 #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	190 penalty='l2',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	191 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	192 #if $method.tl_rank_genes_groups_method.solver.random_state
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	193 random_state=$method.tl_rank_genes_groups_method.solver.random_state,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	194 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	195 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	196 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	197 #else if $method.tl_rank_genes_groups_method.solver.solver == 'saga'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	198 #if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l1'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	199 penalty='l1',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	200 #else if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l2'
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	201 penalty='l2',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	202 #else
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	203 penalty='$method.tl_rank_genes_groups_method.solver.penalty.pen',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	204 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	205 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	206 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	207 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	208 tol=$method.tl_rank_genes_groups_method.tol,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	209 C=$method.tl_rank_genes_groups_method.c,
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	210 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	211 only_positive=$method.only_positive)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	212 pd.options.display.precision = 15
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	213 pd.DataFrame(adata.uns['rank_genes_groups']['names']).to_csv("$names", sep="\t", index = False)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	214 pd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv("$scores", sep="\t", index = False)
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	215 #end if
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	216
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	217 @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	218 ]]></configfile>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	219 </configfiles>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	220 <inputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	221 <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	222 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	223 <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	224 <!--<option value="tl.leiden">, using `tl.leiden`</option>!-->
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	225 <option value="tl.louvain">Cluster cells into subgroups, using `tl.louvain`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	226 <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	227 <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	228 <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	229 <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	230 <option value="tl.umap">Embed the neighborhood graph using UMAP, using `tl.umap`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	231 <!--<option value="tl.phate">, using `tl.phate`</option>!-->
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	232 <option value="pp.neighbors">Compute a neighborhood graph of observations, using `pp.neighbors`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	233 <option value="tl.rank_genes_groups">Rank genes for characterizing groups, using `tl.rank_genes_groups`</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	234 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	235 <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	236 <conditional name="flavor">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	237 <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	238 <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	239 <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	240 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	241 <when value="vtraag">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	242 <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	243 label="Resolution"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	244 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	245 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	246 <when value="igraph"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	247 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	248 <param argument="random_state" type="integer" value="0" label="Random state" help="Change the initialization of the optimization."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	249 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	250 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	251 <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	252 <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	253 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	254 <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	255 <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	256 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	257 <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	258 <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	259 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	260 <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	261 <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	262 <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	263 <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	264 <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	265 <param name="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	266 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	280 <param argument="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	281 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	282 <when value="pp.neighbors">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	283 <param argument="n_neighbors" type="integer" min="0" value="15" label="The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation" help="Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If `knn` is `True`, number of nearest neighbors to be searched. If `knn` is `False`, a Gaussian kernel width is set to the distance of the `n_neighbors` neighbor."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	284 <param argument="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	285 <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the number of neighbors to n_neighbors?" help="If true, it considers a knn graph. Otherwise, it uses a Gaussian Kernel to assign low weights to neighbors more distant than the `n_neighbors` nearest neighbor."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	286 <param argument="random_state" type="integer" value="0" label="Numpy random seed" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	287 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities" help="">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	288 <option value="umap">umap (McInnes et al, 2018)</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	289 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	290 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	291 <param argument="metric" type="select" label="Distance metric" help="">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	292 <expand macro="distance_metric_options"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	293 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	294 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	295 <when value="tl.rank_genes_groups">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	296 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	297 <expand macro="param_use_raw"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	298 <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. ['g1', 'g2', 'g3']. If not passed, a ranking will be generated for all groups."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	299 <conditional name="ref">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	300 <param name="rest" type="select" label="Comparison">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	301 <option value="rest">Compare each group to the union of the rest of the group</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	302 <option value="group_id">Compare with respect to a specific group</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	303 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	304 <when value="rest"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	305 <when value="group_id">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	306 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	307 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	308 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	309 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	310 <conditional name="tl_rank_genes_groups_method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	311 <param argument="method" type="select" label="Method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	312 <option value="t-test">t-test</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	313 <option value="wilcoxon">Wilcoxon-Rank-Sum</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	314 <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	315 <option value="logreg">Logistic regression</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	316 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	317 <when value="t-test"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	318 <when value="wilcoxon"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	319 <when value="t-test_overestim_var"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	320 <when value="logreg">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	321 <conditional name="solver">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	322 <param argument="solver" type="select" label="Algorithm to use in the optimization problem" help="For small datasets, ‘liblinear’ is a good choice, whereas ‘sag’ and ‘saga’ are faster for large ones. For multiclass problems, only ‘newton-cg’, ‘sag’, ‘saga’ and ‘lbfgs’ handle multinomial loss; ‘liblinear’ is limited to one-versus-rest schemes. ‘newton-cg’, ‘lbfgs’ and ‘sag’ only handle L2 penalty, whereas ‘liblinear’ and ‘saga’ handle L1 penalty.">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	323 <option value="newton-cg">newton-cg</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	324 <option value="lbfgs">lbfgs</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	325 <option value="liblinear">liblinear</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	326 <option value="sag">sag</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	327 <option value="saga">saga</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	328 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	329 <when value="newton-cg">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	330 <expand macro="fit_intercept"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	331 <expand macro="max_iter"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	332 <expand macro="multi_class"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	333 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	334 <when value="lbfgs">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	335 <expand macro="fit_intercept"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	336 <expand macro="max_iter"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	337 <expand macro="multi_class"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	338 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	339 <when value="liblinear">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	340 <conditional name="penalty">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	341 <expand macro="penalty"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	342 <when value="l1"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	343 <when value="l2">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	344 <param argument="dual" type="boolean" truevalue="True" falsevalue="False" checked="false"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	345 label="Dual (not primal) formulation?" help="Prefer primal when n_samples > n_features"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	346 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	347 <when value="customized">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	348 <expand macro="custom_penalty"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	349 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	350 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	351 <conditional name="intercept_scaling">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	352 <param argument="fit_intercept" type="select"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	353 label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help="">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	354 <option value="True">Yes</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	355 <option value="False">No</option>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	356 </param>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	357 <when value="True">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	358 <param argument="intercept_scaling" type="float" value="1.0"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	359 label="Intercept scaling"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	360 help="x becomes [x, self.intercept_scaling], i.e. a 'synthetic' feature with constant value equal to intercept_scaling is appended to the instance vector. The intercept becomes intercept_scaling * synthetic_feature_weight."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	361 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	362 <when value="False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	363 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	364 <expand macro="random_state"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	365 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	366 <when value="sag">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	367 <expand macro="fit_intercept"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	368 <expand macro="random_state"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	369 <expand macro="max_iter"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	370 <expand macro="multi_class"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	371 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	372 <when value="saga">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	373 <conditional name="penalty">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	374 <expand macro="penalty"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	375 <when value="l1"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	376 <when value="l2"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	377 <when value="customized">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	378 <expand macro="custom_penalty"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	379 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	380 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	381 <expand macro="fit_intercept"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	382 <expand macro="multi_class"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	383 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	384 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	385 <param argument="tol" type="float" value="1e-4" label="Tolerance for stopping criteria" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	386 <param argument="c" type="float" value="1.0" label="Inverse of regularization strength"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	387 help="It must be a positive float. Like in support vector machines, smaller values specify stronger regularization."/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	388 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	389 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	390 <param argument="only_positive" type="boolean" truevalue="True" falsevalue="False" checked="true"
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	391 label="Only consider positive differences?" help=""/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	392 </when>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	393 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	394 <expand macro="anndata_output_format"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	395 </inputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	396 <outputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	397 <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	398 <data name="X_pca" format="tabular" label="${tool.name} on ${on_string}: PCA representation of data">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	399 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	400 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	401 <data name="PCs" format="tabular" label="${tool.name} on ${on_string}: Principal components containing the loadings">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	402 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	403 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	404 <data name="variance_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratio of explained variance">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	405 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	406 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	407 <data name="variance" format="tabular" label="${tool.name} on ${on_string}: Explained variance, equivalent to the eigenvalues of the covariance matrix">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	408 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	409 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	410 <data name="X_diffmap" format="tabular" label="${tool.name} on ${on_string}: Diffusion map representation">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	411 <filter>method['method'] == 'tl.diffmap'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	412 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	413 <data name="X_tsne" format="tabular" label="${tool.name} on ${on_string}: tSNE coordinates">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	414 <filter>method['method'] == 'tl.tsne'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	415 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	416 <data name="X_umap" format="tabular" label="${tool.name} on ${on_string}: UMAP coordinates">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	417 <filter>method['method'] == 'tl.umap'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	418 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	419 <data name="names" format="tabular" label="${tool.name} on ${on_string}: Gene names">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	420 <filter>method['method'] == 'tl.rank_genes_groups'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	421 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	422 <data name="scores" format="tabular" label="${tool.name} on ${on_string}: Scores">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	423 <filter>method['method'] == 'tl.rank_genes_groups'</filter>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	424 </data>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	425 </outputs>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	426 <tests>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	427 <test expect_num_outputs="1">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	428 <conditional name="input">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	429 <param name="format" value="h5ad" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	430 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	431 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	432 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	433 <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	434 <conditional name="flavor">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	435 <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	436 <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	437 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	438 <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	439 <param name="key_added" value="louvain"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	440 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	441 <param name="anndata_output_format" value="h5ad" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	442 <assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	443 <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	444 <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	445 <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	446 <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	447 <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	448 <has_text_matching expression="key_added='louvain'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	449 </assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	450 <output name="anndata_out_h5ad" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	451 </test>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	452 <test expect_num_outputs="5">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	453 <conditional name="input">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	454 <param name="format" value="h5ad" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	455 <param name="adata" value="krumsiek11.h5ad" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	456 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	457 <conditional name="method">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	458 <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	459 <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	460 <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	461 <conditional name="pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	462 <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	463 <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	464 <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	465 <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	466 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	467 </conditional>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	468 <param name="anndata_output_format" value="h5ad" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	469 <assert_stdout>
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="sc.pp.pca"/>
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="n_comps=50"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	472 <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	473 <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	474 <has_text_matching expression="chunked=False"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	475 <has_text_matching expression="zero_center='True'"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	476 <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	477 <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	478 </assert_stdout>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	479 <output name="anndata_out_h5ad" file="pp.pca.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	480 <output name="X_pca">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	481 <assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	482 <has_text_matching expression="-2.579\d{15}e-01" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	483 <has_text_matching expression="3.452\d{15}e-01" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	484 <has_text_matching expression="-6.088\d{15}e-03" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	485 <has_n_columns n="10" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	486 </assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	487 </output>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	488 <output name="PCs">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	489 <assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	490 <has_text_matching expression="-2.285\d{15}e-01" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	491 <has_text_matching expression="-3.042\d{15}e-01" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	492 <has_text_matching expression="-2.863\d{15}e-02" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	493 <has_text_matching expression="1.294\d{15}e-01" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	494 <has_n_columns n="10" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	495 </assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	496 </output>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	497 <output name="variance_ratio">
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	498 <assert_contents>
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	499 <has_text_matching expression="2.148\d{15}e-01" />
0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	500 <has_text_matching expression="7.596\d{15}e-02" />

0

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1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster and reduce dimension with scanpy" version="@galaxy_version@">

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2 <description></description>

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3 <macros>

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4 <import>macros.xml</import>

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5 <xml name="pca_inputs">

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6 <param name="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/>

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7 <param name="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""/>

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8 <conditional name="pca">

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9 <param name="chunked" type="select" label="Type of PCA?">

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10 <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of `random_seed` and `svd_solver`)</option>

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11 <option value="False" selected="true">Full PCA</option>

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12 </param>

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13 <when value="True">

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14 <param name="chunk_size" type="integer" min="0" value="" label="chunk_size" help="Number of observations to include in each chunk"/>

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15 </when>

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16 <when value="False">

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17 <param name="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"

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18 label="Compute standard PCA from covariance matrix?"

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19 help="If not, it omits zero-centering variables (uses *TruncatedSVD* from scikit-learn), which allows to handle sparse input efficiently."/>

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20 <expand macro="svd_solver"/>

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21 <param name="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>

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22 </when>

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23 </conditional>

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24 </xml>

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25 <token name="@CMD_pca_outputs@"><![CDATA[

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26 np.savetxt('$X_pca', adata.obsm['X_pca'], delimiter='\t')

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27 np.savetxt('$PCs', adata.varm['PCs'], delimiter='\t')

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28 np.savetxt('$variance', adata.uns['pca']['variance'], delimiter='\t')

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29 np.savetxt('$variance_ratio', adata.uns['pca']['variance_ratio'], delimiter='\t')

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30 ]]></token>

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31 <token name="@CMD_pca_params@"><![CDATA[

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32 data=adata,

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33 n_comps=$method.n_comps,

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34 dtype='$method.dtype',

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35 copy=False,

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36 chunked=$method.pca.chunked,

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37 #if $method.pca.chunked == 'True'

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38 chunk_size=$method.pca.chunk_size

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39 #else

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40 zero_center='$method.pca.zero_center',

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41 svd_solver='$method.pca.svd_solver',

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42 random_state=$method.pca.random_state

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43 #end if

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44 ]]></token>

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45 <xml name="penalty">

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46 <param argument="penalty" type="select" label="Norm used in the penalization" help="">

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47 <option value="l1">l1</option>

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48 <option value="l2">l2</option>

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49 <option value="customized">customized</option>

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50 </param>

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51 </xml>

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52 <xml name="custom_penalty">

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53 <param argument="pen" type="text" value="" label="Norm used in the penalization" help=""/>

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54 </xml>

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55 <xml name="fit_intercept">

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56 <param argument="fit_intercept" type="boolean" truevalue="True" falsevalue="False" checked="true"

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57 label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help=""/>

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58 </xml>

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59 <xml name="random_state">

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60 <param argument="random_state" type="integer" value="" optional="true"

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61 label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>

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62 </xml>

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63 <xml name="max_iter">

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64 <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge" help=""/>

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65 </xml>

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66 <xml name="multi_class">

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67 <param argument="multi_class" type="select" label="Multi class" help="">

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68 <option value="ovr">ovr: a binary problem is fit for each label</option>

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69 <option value="multinomial">multinomial: the multinomial loss fit across the entire probability distribution, even when the data is binary</option>

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70 <option value="auto">auto: selects ‘ovr’ if the data is binary and otherwise selects ‘multinomial’</option>

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71 </param>

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72 </xml>

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73 </macros>

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74 <expand macro="requirements"/>

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75 <expand macro="version_command"/>

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76 <command detect_errors="exit_code"><![CDATA[

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77 @CMD@

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78 ]]></command>

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79 <configfiles>

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80 <configfile name="script_file"><![CDATA[

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81 @CMD_imports@

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82 @CMD_read_inputs@

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83

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84 #if $method.method == 'tl.louvain'

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85 sc.tl.louvain(

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86 adata=adata,

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87 flavor = '$method.flavor.flavor',

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88 #if $method.flavor.flavor == 'vtraag' and $method.flavor.resolution

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89 resolution=$method.flavor.resolution,

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90 #end if

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91 random_state=$method.random_state,

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92 key_added='$method.key_added',

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93 copy=False)

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94 #elif $method.method == 'pp.pca'

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95 sc.pp.pca(@CMD_pca_params@)

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96 @CMD_pca_outputs@

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97 #elif $method.method == 'tl.pca'

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98 sc.tl.pca(@CMD_pca_params@)

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99 @CMD_pca_outputs@

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100 #elif $method.method == 'tl.diffmap'

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101 sc.tl.diffmap(

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102 adata=adata,

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103 n_comps=$method.n_comps,

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104 copy =False)

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105 np.savetxt('$X_diffmap', adata.obsm['X_diffmap'], delimiter='\t')

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106 #elif $method.method == 'tl.tsne'

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107 sc.tl.tsne(

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108 adata=adata,

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109 #if $method.n_pcs

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110 n_pcs=$method.n_pcs,

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111 #end if

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112 perplexity=$method.perplexity,

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113 early_exaggeration=$method.early_exaggeration,

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114 learning_rate=$method.learning_rate,

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115 random_state=$method.random_state,

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116 copy=False)

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117 np.savetxt('$X_tsne', adata.obsm['X_tsne'], delimiter='\t')

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118 #elif $method.method == 'tl.umap'

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119 sc.tl.umap(

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120 adata=adata,

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121 min_dist=$method.min_dist,

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122 spread=$method.spread,

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123 n_components=$method.n_components,

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124 #if $method.maxiter

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125 maxiter=$method.maxiter,

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126 #end if

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127 alpha=$method.alpha,

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128 gamma=$method.gamma,

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129 negative_sample_rate=$method.negative_sample_rate,

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130 init_pos='$method.init_pos',

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131 random_state=$method.random_state,

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132 copy=False)

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133 np.savetxt('$X_umap', adata.obsm['X_umap'], delimiter='\t')

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134 #elif $method.method == 'pp.neighbors'

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135 sc.pp.neighbors(

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136 adata=adata,

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137 n_neighbors=$method.n_neighbors,

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138 #if $method.n_pcs

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139 n_pcs=$method.n_pcs,

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140 #end if

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141 knn=$method.knn,

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142 random_state=$method.random_state,

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143 method='$method.pp_neighbors_method',

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144 metric='$method.metric',

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145 copy=False)

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146 #elif $method.method == 'tl.rank_genes_groups'

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147 sc.tl.rank_genes_groups(

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148 adata=adata,

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149 groupby='$method.groupby',

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150 use_raw=$method.use_raw,

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151 #if str($method.groups) != ''

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152 groups='$method.groups',

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153 #end if

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154 #if $method.ref.rest == 'rest'

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155 reference='$method.ref.rest',

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156 #else

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157 reference='$method.ref.reference',

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158 #end if

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159 n_genes=$method.n_genes,

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160 method='$method.tl_rank_genes_groups_method.method',

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161 #if $method.tl_rank_genes_groups_method.method == 'logreg'

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162 solver='$method.tl_rank_genes_groups_method.solver.solver',

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163 #if $method.tl_rank_genes_groups_method.solver.solver == 'newton-cg'

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164 penalty='l2',

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165 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,

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166 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,

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167 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',

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168 #else if $method.tl_rank_genes_groups_method.solver.solver == 'lbfgs'

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169 penalty='l2',

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170 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,

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171 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,

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172 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',

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173 #else if $method.tl_rank_genes_groups_method.solver.solver == 'liblinear'

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174 #if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l1'

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175 penalty='l1',

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176 #else if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l2'

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177 penalty='l2',

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178 dual=$method.tl_rank_genes_groups_method.solver.penalty.dual,

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179 #else

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180 penalty='$method.tl_rank_genes_groups_method.solver.penalty.pen',

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181 #end if

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182 fit_intercept=$method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept,

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183 #if $method.tl_rank_genes_groups_method.solver.intercept_scaling.fit_intercept == 'True'

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184 intercept_scaling=$method.tl_rank_genes_groups_method.solver.intercept_scaling.intercept_scaling,

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185 #end if

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186 #if $method.tl_rank_genes_groups_method.solver.random_state

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187 random_state=$method.tl_rank_genes_groups_method.solver.random_state,

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188 #end if

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189 #else if $method.tl_rank_genes_groups_method.solver.solver == 'sag'

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190 penalty='l2',

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191 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,

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192 #if $method.tl_rank_genes_groups_method.solver.random_state

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193 random_state=$method.tl_rank_genes_groups_method.solver.random_state,

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194 #end if

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195 max_iter=$method.tl_rank_genes_groups_method.solver.max_iter,

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196 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',

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197 #else if $method.tl_rank_genes_groups_method.solver.solver == 'saga'

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198 #if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l1'

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199 penalty='l1',

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200 #else if $method.tl_rank_genes_groups_method.solver.penalty.penalty == 'l2'

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201 penalty='l2',

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202 #else

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203 penalty='$method.tl_rank_genes_groups_method.solver.penalty.pen',

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204 #end if

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205 fit_intercept=$method.tl_rank_genes_groups_method.solver.fit_intercept,

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206 multi_class='$method.tl_rank_genes_groups_method.solver.multi_class',

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207 #end if

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208 tol=$method.tl_rank_genes_groups_method.tol,

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209 C=$method.tl_rank_genes_groups_method.c,

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210 #end if

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211 only_positive=$method.only_positive)

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212 pd.options.display.precision = 15

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213 pd.DataFrame(adata.uns['rank_genes_groups']['names']).to_csv("$names", sep="\t", index = False)

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214 pd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv("$scores", sep="\t", index = False)

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215 #end if

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216

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217 @CMD_anndata_write_outputs@

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218 ]]></configfile>

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219 </configfiles>

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220 <inputs>

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221 <expand macro="inputs_anndata"/>

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222 <conditional name="method">

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223 <param argument="method" type="select" label="Method used for plotting">

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224

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225 <option value="tl.louvain">Cluster cells into subgroups, using `tl.louvain`</option>

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226 <option value="pp.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`</option>

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227 <option value="tl.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca`</option>

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228 <option value="tl.diffmap">Diffusion Maps, using `tl.diffmap`</option>

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229 <option value="tl.tsne">t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`</option>

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230 <option value="tl.umap">Embed the neighborhood graph using UMAP, using `tl.umap`</option>

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231

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232 <option value="pp.neighbors">Compute a neighborhood graph of observations, using `pp.neighbors`</option>

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233 <option value="tl.rank_genes_groups">Rank genes for characterizing groups, using `tl.rank_genes_groups`</option>

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234 </param>

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235 <when value="tl.louvain">

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236 <conditional name="flavor">

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237 <param argument="flavor" type="select" label="Flavor for the clustering" help="">

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238 <option value="vtraag">vtraag (much more powerful)</option>

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239 <option value="igraph">igraph</option>

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240 </param>

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241 <when value="vtraag">

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242 <param argument="resolution" type="float" value="" optional="true"

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243 label="Resolution"

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244 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"/>

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245 </when>

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246 <when value="igraph"/>

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247 </conditional>

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248 <param argument="random_state" type="integer" value="0" label="Random state" help="Change the initialization of the optimization."/>

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249 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help=""/>

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250 </when>

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251 <when value="pp.pca">

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252 <expand macro="pca_inputs"/>

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253 </when>

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254 <when value="tl.pca">

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255 <expand macro="pca_inputs"/>

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256 </when>

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257 <when value="tl.diffmap">

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258 <param argument="n_comps" type="integer" min="0" value="15" optional="true" label="Number of dimensions of the representation" help=""/>

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259 </when>

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260 <when value="tl.tsne">

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261 <param name="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>

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262 <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."/>

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263 <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."/>

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264 <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."/>

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265 <param name="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>

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266 </when>

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267 <when value="tl.umap">

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268 <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."/>

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269 <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."/>

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270 <param argument="n_components" type="integer" min="0" value="2" label="Number of dimensions of the embedding" help=""/>

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271 <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."/>

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272 <param argument="alpha" type="float" value="1.0" label="Initial learning rate for the embedding optimization" help=""/>

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273 <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."/>

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274 <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=""/>

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275 <param argument="init_pos" type="select" label="How to initialize the low dimensional embedding" help="Called `init` in the original UMAP">

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276 <option value="paga">Position from paga</option>

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277 <option value="spectral" selected="true">Spectral embedding of the graph</option>

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278 <option value="random">Initial embedding positions at random</option>

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279 </param>

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280 <param argument="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>

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281 </when>

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282 <when value="pp.neighbors">

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283 <param argument="n_neighbors" type="integer" min="0" value="15" label="The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation" help="Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If `knn` is `True`, number of nearest neighbors to be searched. If `knn` is `False`, a Gaussian kernel width is set to the distance of the `n_neighbors` neighbor."/>

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284 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>

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285 <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the number of neighbors to n_neighbors?" help="If true, it considers a knn graph. Otherwise, it uses a Gaussian Kernel to assign low weights to neighbors more distant than the `n_neighbors` nearest neighbor."/>

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286 <param argument="random_state" type="integer" value="0" label="Numpy random seed" help=""/>

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287 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities" help="">

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288 <option value="umap">umap (McInnes et al, 2018)</option>

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289 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option>

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290 </param>

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291 <param argument="metric" type="select" label="Distance metric" help="">

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292 <expand macro="distance_metric_options"/>

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293 </param>

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294 </when>

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295 <when value="tl.rank_genes_groups">

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296 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help=""/>

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297 <expand macro="param_use_raw"/>

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298 <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. ['g1', 'g2', 'g3']. If not passed, a ranking will be generated for all groups."/>

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299 <conditional name="ref">

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300 <param name="rest" type="select" label="Comparison">

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301 <option value="rest">Compare each group to the union of the rest of the group</option>

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302 <option value="group_id">Compare with respect to a specific group</option>

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303 </param>

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304 <when value="rest"/>

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305 <when value="group_id">

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306 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare"/>

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307 </when>

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308 </conditional>

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309 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>

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310 <conditional name="tl_rank_genes_groups_method">

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311 <param argument="method" type="select" label="Method">

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312 <option value="t-test">t-test</option>

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313 <option value="wilcoxon">Wilcoxon-Rank-Sum</option>

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314 <option value="t-test_overestim_var" selected="true">t-test with overestimate of variance of each group</option>

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315 <option value="logreg">Logistic regression</option>

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316 </param>

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317 <when value="t-test"/>

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318 <when value="wilcoxon"/>

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319 <when value="t-test_overestim_var"/>

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320 <when value="logreg">

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321 <conditional name="solver">

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322 <param argument="solver" type="select" label="Algorithm to use in the optimization problem" help="For small datasets, ‘liblinear’ is a good choice, whereas ‘sag’ and ‘saga’ are faster for large ones. For multiclass problems, only ‘newton-cg’, ‘sag’, ‘saga’ and ‘lbfgs’ handle multinomial loss; ‘liblinear’ is limited to one-versus-rest schemes. ‘newton-cg’, ‘lbfgs’ and ‘sag’ only handle L2 penalty, whereas ‘liblinear’ and ‘saga’ handle L1 penalty.">

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323 <option value="newton-cg">newton-cg</option>

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324 <option value="lbfgs">lbfgs</option>

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325 <option value="liblinear">liblinear</option>

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326 <option value="sag">sag</option>

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327 <option value="saga">saga</option>

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328 </param>

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329 <when value="newton-cg">

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330 <expand macro="fit_intercept"/>

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331 <expand macro="max_iter"/>

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332 <expand macro="multi_class"/>

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333 </when>

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334 <when value="lbfgs">

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335 <expand macro="fit_intercept"/>

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336 <expand macro="max_iter"/>

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337 <expand macro="multi_class"/>

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338 </when>

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339 <when value="liblinear">

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340 <conditional name="penalty">

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341 <expand macro="penalty"/>

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342 <when value="l1"/>

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343 <when value="l2">

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344 <param argument="dual" type="boolean" truevalue="True" falsevalue="False" checked="false"

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345 label="Dual (not primal) formulation?" help="Prefer primal when n_samples > n_features"/>

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346 </when>

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347 <when value="customized">

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348 <expand macro="custom_penalty"/>

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349 </when>

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350 </conditional>

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351 <conditional name="intercept_scaling">

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352 <param argument="fit_intercept" type="select"

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353 label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help="">

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354 <option value="True">Yes</option>

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355 <option value="False">No</option>

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356 </param>

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357 <when value="True">

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358 <param argument="intercept_scaling" type="float" value="1.0"

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359 label="Intercept scaling"

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360 help="x becomes [x, self.intercept_scaling], i.e. a 'synthetic' feature with constant value equal to intercept_scaling is appended to the instance vector. The intercept becomes intercept_scaling * synthetic_feature_weight."/>

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361 </when>

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362 <when value="False"/>

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363 </conditional>

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364 <expand macro="random_state"/>

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365 </when>

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366 <when value="sag">

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367 <expand macro="fit_intercept"/>

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368 <expand macro="random_state"/>

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369 <expand macro="max_iter"/>

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370 <expand macro="multi_class"/>

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371 </when>

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372 <when value="saga">

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373 <conditional name="penalty">

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374 <expand macro="penalty"/>

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375 <when value="l1"/>

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376 <when value="l2"/>

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377 <when value="customized">

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378 <expand macro="custom_penalty"/>

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379 </when>

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380 </conditional>

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381 <expand macro="fit_intercept"/>

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382 <expand macro="multi_class"/>

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383 </when>

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384 </conditional>

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385 <param argument="tol" type="float" value="1e-4" label="Tolerance for stopping criteria" help=""/>

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386 <param argument="c" type="float" value="1.0" label="Inverse of regularization strength"

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387 help="It must be a positive float. Like in support vector machines, smaller values specify stronger regularization."/>

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388 </when>

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389 </conditional>

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390 <param argument="only_positive" type="boolean" truevalue="True" falsevalue="False" checked="true"

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391 label="Only consider positive differences?" help=""/>

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392 </when>

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393 </conditional>

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394 <expand macro="anndata_output_format"/>

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395 </inputs>

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396 <outputs>

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397 <expand macro="anndata_outputs"/>

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398 <data name="X_pca" format="tabular" label="${tool.name} on ${on_string}: PCA representation of data">

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399 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>

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400 </data>

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401 <data name="PCs" format="tabular" label="${tool.name} on ${on_string}: Principal components containing the loadings">

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402 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>

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403 </data>

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404 <data name="variance_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratio of explained variance">

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405 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>

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406 </data>

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407 <data name="variance" format="tabular" label="${tool.name} on ${on_string}: Explained variance, equivalent to the eigenvalues of the covariance matrix">

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408 <filter>method['method'] == 'pp.pca' or method['method'] == 'tl.pca'</filter>

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409 </data>

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410 <data name="X_diffmap" format="tabular" label="${tool.name} on ${on_string}: Diffusion map representation">

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411 <filter>method['method'] == 'tl.diffmap'</filter>

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412 </data>

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413 <data name="X_tsne" format="tabular" label="${tool.name} on ${on_string}: tSNE coordinates">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

414 <filter>method['method'] == 'tl.tsne'</filter>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

415 </data>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

416 <data name="X_umap" format="tabular" label="${tool.name} on ${on_string}: UMAP coordinates">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

417 <filter>method['method'] == 'tl.umap'</filter>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

418 </data>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

419 <data name="names" format="tabular" label="${tool.name} on ${on_string}: Gene names">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

420 <filter>method['method'] == 'tl.rank_genes_groups'</filter>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

421 </data>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

422 <data name="scores" format="tabular" label="${tool.name} on ${on_string}: Scores">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

423 <filter>method['method'] == 'tl.rank_genes_groups'</filter>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

424 </data>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

425 </outputs>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

426 <tests>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

427 <test expect_num_outputs="1">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

428 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

429 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

430 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

431 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

432 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

433 <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

434 <conditional name="flavor">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

435 <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

436 <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

437 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

438 <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

439 <param name="key_added" value="louvain"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

440 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

441 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

442 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

443 <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

444 <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

445 <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

446 <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

447 <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

448 <has_text_matching expression="key_added='louvain'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

449 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

450 <output name="anndata_out_h5ad" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

451 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

452 <test expect_num_outputs="5">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

453 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

454 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

455 <param name="adata" value="krumsiek11.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

456 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

457 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

458 <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

459 <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

460 <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

461 <conditional name="pca">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

462 <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

463 <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

464 <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

465 <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

466 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

467 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

468 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

469 <assert_stdout>

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="sc.pp.pca"/>

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="n_comps=50"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

472 <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

473 <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

474 <has_text_matching expression="chunked=False"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

475 <has_text_matching expression="zero_center='True'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

476 <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

477 <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

478 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

479 <output name="anndata_out_h5ad" file="pp.pca.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

480 <output name="X_pca">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

481 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

482 <has_text_matching expression="-2.579\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

483 <has_text_matching expression="3.452\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

484 <has_text_matching expression="-6.088\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

485 <has_n_columns n="10" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

486 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

487 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

488 <output name="PCs">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

489 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

490 <has_text_matching expression="-2.285\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

491 <has_text_matching expression="-3.042\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

492 <has_text_matching expression="-2.863\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

493 <has_text_matching expression="1.294\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

494 <has_n_columns n="10" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

495 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

496 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

497 <output name="variance_ratio">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

498 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

499 <has_text_matching expression="2.148\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

500 <has_text_matching expression="7.596\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

501 <has_text_matching expression="5.033\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

502 <has_text_matching expression="2.801\d{15}e-05" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

503 <has_n_columns n="1" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

504 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

505 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

506 <output name="variance" file="pp.pca.variance.krumsiek11.tabular" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

507 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

508 <test expect_num_outputs="5">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

509 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

510 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

511 <param name="adata" value="krumsiek11.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

512 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

513 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

514 <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

515 <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

516 <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

517 <conditional name="pca">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

518 <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

519 <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

520 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

521 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

522 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

523 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

524 <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

525 <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

526 <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

527 <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

528 <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

529 <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

530 <has_text_matching expression="chunk_size=50"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

531 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

532 <output name="anndata_out_h5ad" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

533 <output name="X_pca">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

534 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

535 <has_text_matching expression="1.290\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

536 <has_text_matching expression="9.231\d{15}e-04" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

537 <has_text_matching expression="-3.498\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

538 <has_text_matching expression="-4.921\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

539 <has_n_columns n="10" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

540 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

541 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

542 <output name="PCs">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

543 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

544 <has_text_matching expression="2.35298924\d\d\d\d\d\d\d\d\d\de-0\d" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

545 <has_text_matching expression="2.4286999\d\d\d\d\d\d\d\d\d\d\de-0\d" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

546 <has_n_columns n="10" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

547 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

548 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

549 <output name="variance_ratio">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

550 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

551 <has_text text="6.4362" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

552 <has_text text="2.7348" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

553 <has_n_columns n="1" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

554 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

555 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

556 <output name="variance">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

557 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

558 <has_text_matching expression="7.540\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

559 <has_text_matching expression="1.173\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

560 <has_text_matching expression="3.204\d{15}e-05" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

561 <has_n_columns n="1" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

562 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

563 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

564 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

565 <test expect_num_outputs="5">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

566 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

567 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

568 <param name="adata" value="krumsiek11.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

569 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

570 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

571 <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

572 <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

573 <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

574 <conditional name="pca">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

575 <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

576 <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

577 <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

578 <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

579 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

580 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

581 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

582 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

583 <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

584 <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

585 <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

586 <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

587 <has_text_matching expression="chunked=False"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

588 <has_text_matching expression="zero_center='True'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

589 <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

590 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

591 <output name="anndata_out_h5ad" file="tl.pca.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

592 <output name="X_pca">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

593 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

594 <has_text_matching expression="-6.366\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

595 <has_text_matching expression="5.702\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

596 <has_text_matching expression="1.862\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

597 <has_text_matching expression="-6.861\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

598 <has_n_columns n="10" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

599 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

600 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

601 <output name="PCs">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

602 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

603 <has_text_matching expression="1.341\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

604 <has_text_matching expression="-3.478\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

605 <has_text_matching expression="-4.890\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

606 <has_text_matching expression="-2.628\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

607 <has_n_columns n="10" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

608 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

609 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

610 <output name="variance_ratio">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

611 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

612 <has_text_matching expression="6.436\d{15}e-01" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

613 <has_text_matching expression="1.316\d{15}e-04" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

614 <has_text_matching expression="2.801\d{15}e-05" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

615 <has_n_columns n="1" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

616 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

617 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

618 <output name="variance">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

619 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

620 <has_text_matching expression="4.575\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

621 <has_text_matching expression="2.166\d{15}e-02" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

622 <has_text_matching expression="5.896\d{15}e-03" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

623 <has_n_columns n="1" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

624 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

625 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

626 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

627 <test expect_num_outputs="2">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

628 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

629 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

630 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

631 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

632 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

633 <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

634 <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

635 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

636 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

637 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

638 <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

639 <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

640 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

641 <output name="anndata_out_h5ad" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

642 <output name="X_diffmap" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.X_diffmap.tabular"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

643 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

644 <test expect_num_outputs="2">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

645 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

646 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

647 <param name="adata" value="krumsiek11.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

648 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

649 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

650 <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

651 <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

652 <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

653 <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

654 <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

655 <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

656 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

657 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

658 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

659 <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

660 <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

661 <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

662 <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

663 <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

664 <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

665 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

666 <output name="anndata_out_h5ad" file="tl.tsne.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

667 <output name="X_tsne" file="tl.tsne.krumsiek11_X_tsne.tabular"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

668 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

669 <test expect_num_outputs="2" >

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

670 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

671 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

672 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

673 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

674 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

675 <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

676 <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

677 <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

678 <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

679 <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

680 <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

681 <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

682 <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

683 <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

684 <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

685 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

686 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

687 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

688 <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

689 <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

690 <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

691 <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

692 <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

693 <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

694 <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

695 <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

696 <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

697 <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

698 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

699 <output name="anndata_out_h5ad" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

700 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

701 <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

702 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

703 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

704 <output name="X_umap">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

705 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

706 <has_text text="2.31791388" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

707 <has_text text="-4.8602690" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

708 <has_text text="-1.8031970" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

709 <has_text text="2.31166780" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

710 <has_n_columns n="2" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

711 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

712 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

713 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

714 <test expect_num_outputs="1">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

715 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

716 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

717 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

718 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

719 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

720 <param name="method" value="pp.neighbors"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

721 <param name="n_neighbors" value="15"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

722 <param name="knn" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

723 <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

724 <param name="pp_neighbors_method" value="umap"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

725 <param name="metric" value="euclidean"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

726 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

727 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

728 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

729 <has_text_matching expression="sc.pp.neighbors"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

730 <has_text_matching expression="n_neighbors=15"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

731 <has_text_matching expression="knn=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

732 <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

733 <has_text_matching expression="method='umap'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

734 <has_text_matching expression="metric='euclidean'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

735 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

736 <output name="anndata_out_h5ad" file="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

737 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

738 <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

739 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

740 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

741 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

742 <test expect_num_outputs="1">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

743 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

744 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

745 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

746 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

747 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

748 <param name="method" value="pp.neighbors"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

749 <param name="n_neighbors" value="15"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

750 <param name="knn" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

751 <param name="pp_neighbors_method" value="gauss"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

752 <param name="metric" value="braycurtis"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

753 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

754 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

755 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

756 <has_text_matching expression="sc.pp.neighbors"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

757 <has_text_matching expression="n_neighbors=15"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

758 <has_text_matching expression="knn=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

759 <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

760 <has_text_matching expression="method='gauss'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

761 <has_text_matching expression="metric='braycurtis'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

762 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

763 <output name="anndata_out_h5ad" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

764 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

765 <test expect_num_outputs="3">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

766 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

767 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

768 <param name="adata" value="krumsiek11.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

769 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

770 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

771 <param name="method" value="tl.rank_genes_groups"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

772 <param name="groupby" value="cell_type"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

773 <param name="use_raw" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

774 <conditional name="ref">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

775 <param name="rest" value="rest"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

776 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

777 <param name="n_genes" value="100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

778 <conditional name="tl_rank_genes_groups_method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

779 <param name="method" value="t-test_overestim_var"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

780 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

781 <param name="only_positive" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

782 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

783 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

784 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

785 <has_text_matching expression="sc.tl.rank_genes_groups"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

786 <has_text_matching expression="groupby='cell_type'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

787 <has_text_matching expression="use_raw=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

788 <has_text_matching expression="reference='rest'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

789 <has_text_matching expression="n_genes=100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

790 <has_text_matching expression="method='t-test_overestim_var'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

791 <has_text_matching expression="only_positive=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

792 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

793 <output name="anndata_out_h5ad" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

794 <output name="names">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

795 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

796 <has_n_columns n="5" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

797 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

798 <has_text_matching expression="Gata1\tFog1\tCebpa\tFli1\tGata2"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

799 <has_text_matching expression="EgrNab\tEgrNab\tSCL\tSCL\tGfi1"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

800 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

801 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

802 <output name="scores">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

803 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

804 <has_n_columns n="5" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

805 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

806 <has_text_matching expression="18.86\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

807 <has_text_matching expression="17.85\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

808 <has_text_matching expression="-2.63\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

809 <has_text_matching expression="-2.98\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

810 <has_text_matching expression="-6.41\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

811 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

812 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

813 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

814 <test expect_num_outputs="3">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

815 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

816 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

817 <param name="adata" value="pbmc68k_reduced.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

818 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

819 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

820 <param name="method" value="tl.rank_genes_groups"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

821 <param name="groupby" value="louvain"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

822 <param name="use_raw" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

823 <conditional name="ref">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

824 <param name="rest" value="rest"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

825 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

826 <param name="n_genes" value="100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

827 <conditional name="tl_rank_genes_groups_method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

828 <param name="method" value="logreg"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

829 <conditional name="solver">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

830 <param name="solver" value="newton-cg"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

831 <param name="fit_intercept" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

832 <param name="max_iter" value="100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

833 <param name="multi_class" value="auto"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

834 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

835 <param name="tol" value="1e-4"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

836 <param name="c" value="1.0"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

837 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

838 <param name="only_positive" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

839 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

840 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

841 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

842 <has_text_matching expression="sc.tl.rank_genes_groups"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

843 <has_text_matching expression="groupby='louvain'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

844 <has_text_matching expression="use_raw=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

845 <has_text_matching expression="reference='rest'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

846 <has_text_matching expression="n_genes=100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

847 <has_text_matching expression="method='logreg'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

848 <has_text_matching expression="solver='newton-cg'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

849 <has_text_matching expression="penalty='l2'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

850 <has_text_matching expression="fit_intercept=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

851 <has_text_matching expression="max_iter=100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

852 <has_text_matching expression="multi_class='auto'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

853 <has_text_matching expression="tol=0.0001"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

854 <has_text_matching expression="C=1.0"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

855 <has_text_matching expression="only_positive=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

856 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

857 <output name="anndata_out_h5ad" ftype="h5">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

858 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

859 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

860 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

861 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

862 <output name="names">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

863 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

864 <has_n_columns n="7" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

865 <has_text_matching expression="IL32\tFCGR3A\tFCER1A\tLTB\tCPVL\tIGJ\tPRSS57"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

866 <has_text_matching expression="KIAA0101\tFCER1G\tHLA-DMA\tHLA-DQA1\tNAAA\tMANF\tCCDC104"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

867 <has_text_matching expression="CCNB2\t"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

868 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

869 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

870 <output name="scores">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

871 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

872 <has_n_columns n="7" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

873 <has_text_matching expression="0.088\d+"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

874 <has_text_matching expression="0.114\d+"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

875 <has_text_matching expression="0.034\d+"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

876 <has_text_matching expression="0.035\d+"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

877 <has_text_matching expression="0.041\d+"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

878 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

879 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

880 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

881 <test expect_num_outputs="3">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

882 <conditional name="input">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

883 <param name="format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

884 <param name="adata" value="pbmc68k_reduced.h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

885 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

886 <conditional name="method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

887 <param name="method" value="tl.rank_genes_groups"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

888 <param name="groupby" value="louvain"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

889 <param name="use_raw" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

890 <conditional name="ref">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

891 <param name="rest" value="rest"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

892 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

893 <param name="n_genes" value="100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

894 <conditional name="tl_rank_genes_groups_method">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

895 <param name="method" value="logreg"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

896 <conditional name="solver">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

897 <param name="solver" value="liblinear"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

898 <conditional name="penalty">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

899 <param name="penalty" value="l2"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

900 <param name="dual" value="False"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

901 <conditional name="intercept_scaling">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

902 <param name="fit_intercept" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

903 <param name="intercept_scaling" value="1.0" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

904 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

905 <param name="random_state" value="1"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

906 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

907 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

908 <param name="tol" value="1e-4"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

909 <param name="c" value="1.0"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

910 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

911 <param name="only_positive" value="True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

912 </conditional>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

913 <param name="anndata_output_format" value="h5ad" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

914 <assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

915 <has_text_matching expression="sc.tl.rank_genes_groups"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

916 <has_text_matching expression="groupby='louvain'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

917 <has_text_matching expression="use_raw=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

918 <has_text_matching expression="reference='rest'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

919 <has_text_matching expression="n_genes=100"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

920 <has_text_matching expression="method='logreg'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

921 <has_text_matching expression="solver='liblinear'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

922 <has_text_matching expression="penalty='l2'"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

923 <has_text_matching expression="dual=False"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

924 <has_text_matching expression="fit_intercept=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

925 <has_text_matching expression="intercept_scaling=1.0"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

926 <has_text_matching expression="tol=0.0001"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

927 <has_text_matching expression="C=1.0"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

928 <has_text_matching expression="only_positive=True"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

929 </assert_stdout>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

930 <output name="anndata_out_h5ad" ftype="h5">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

931 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

932 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

933 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

934 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

935 <output name="names">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

936 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

937 <has_n_columns n="7" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

938 <has_text_matching expression="AES\tLST1\tRNASE6\tPLAC8\tCST3\tSEC11C\tNASP"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

939 <has_text_matching expression="GIMAP4\tMIS18BP1\tLILRB4\tTUBA4A\tCOMTD1\tSLC25A4\tLEPROT"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

940 <has_text_matching expression="GGH\tLYN\tMAGOHB\tAL928768.3\tITGB2-AS1\tCENPH\tASRGL1"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

941 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

942 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

943 <output name="scores">

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

944 <assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

945 <has_n_columns n="7" />

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

946 <has_text_matching expression="0.1680\d{4}\t0.2156\d{4}\t0.281\d{4}\t0.2100\d{4}\t0.2332\d{4}\t0.1586\d{4}\t0.12057\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

947 <has_text_matching expression="0.0784\d{4}\t0.0699\d{4}\t0.06912\d{4}\t0.05364\d{4}\t0.03933\d{4}\t0.03994\d{4}\t0.0411\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

948 <has_text_matching expression="0.06232\d{4}\t0.05563\d{4}\t0.0565\d{4}\t0.04164\d{4}\t0.02636\d{4}\t0.03002\d{4}\t0.032\d{4}"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

949 </assert_contents>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

950 </output>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

951 </test>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

952 </tests>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

953 <help><![CDATA[

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

954 Cluster cells into subgroups, using `tl.louvain`

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

955 ================================================

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956

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957 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation

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958 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell

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959 analysis by Levine et al, 2015.

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960

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961 This requires to run `pp.neighbors`, first.

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962

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963 More details on the `scanpy documentation

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964 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.louvain.html#scanpy.api.tl.louvain>`_

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965

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966 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca`

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967 ============================================================================================================

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968

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969 It uses the implementation of *scikit-learn*.

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970

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971 More details on the `scanpy documentation

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972 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.pca.html#scanpy.api.pp.pca>`__

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973

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974 Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca`

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975 ============================================================================================================

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976

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977 It uses the implementation of *scikit-learn*.

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978

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979 Diffusion Maps

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980

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981 More details on the `scanpy documentation

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982 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.pca.html#scanpy.api.tl.pca>`__

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983

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984 Diffusion Maps, using `tl.diffmap`

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985 ==================================

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986

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987 Diffusion maps (Coifman et al 2005) has been proposed for visualizing single-cell

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988 data by Haghverdi et al (2015). The tool uses the adapted Gaussian kernel suggested

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989 by Haghverdi et al (2016) in the implementation of Wolf et al (2017).

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990

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991 The width ("sigma") of the connectivity kernel is implicitly determined by

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992 the number of neighbors used to compute the single-cell graph in

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993 `pp.neighbors`. To reproduce the original implementation

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994 using a Gaussian kernel, use `method=='gauss'` in

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995 `pp.neighbors`. To use an exponential kernel, use the default

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996 `method=='umap'`. Differences between these options shouldn't usually be

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997 dramatic.

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998

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999 It returns `X_diffmap`, diffusion map representation of data, which is the right eigen basis of the transition matrix with eigenvectors as columns.

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1000

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1001 More details on the `scanpy documentation

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1002 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.diffmap.html#scanpy.api.tl.diffmap>`__

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1003

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1004 t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`

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1005 =======================================================================

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1006

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1007 t-distributed stochastic neighborhood embedding (tSNE) (Maaten et al, 2008) has been

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1008 proposed for visualizating single-cell data by (Amir et al, 2013). Here, by default,

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1009 we use the implementation of *scikit-learn* (Pedregosa et al, 2011).

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1010

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1011 It returns `X_tsne`, tSNE coordinates of data.

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1012

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1013 More details on the `scanpy documentation

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1014 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.tsne.html#scanpy.api.tl.tsne>`__

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1015

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1016 Embed the neighborhood graph using UMAP, using `tl.umap`

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1017 ========================================================

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1018

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1019 UMAP (Uniform Manifold Approximation and Projection) is a manifold learning

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1020 technique suitable for visualizing high-dimensional data. Besides tending to

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1021 be faster than tSNE, it optimizes the embedding such that it best reflects

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1022 the topology of the data, which we represent throughout Scanpy using a

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1023 neighborhood graph. tSNE, by contrast, optimizes the distribution of

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1024 nearest-neighbor distances in the embedding such that these best match the

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1025 distribution of distances in the high-dimensional space. We use the

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1026 implementation of `umap-learn <https://github.com/lmcinnes/umap>`__

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1027 (McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint

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1028 <https://doi.org/10.1101/298430>`__.

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1029

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1030 It returns `X_umap`, UMAP coordinates of data.

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1031

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1032 More details on the `scanpy documentation

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1033 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.umap.html#scanpy.api.tl.umap>`__

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1034

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1035 Compute a neighborhood graph of observations, using `pp.neighbors`

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1036 ==================================================================

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1037

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1038 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),

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1039 which also provides a method for estimating connectivities of data points -

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1040 the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`,

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1041 connectivities are computed according to Coifman et al (2005), in the adaption of

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1042 Haghverdi et al (2016).

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1043

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1044 More details on the `scanpy documentation

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1045 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.neighbors.html#scanpy.api.pp.neighbors>`__

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1046

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1047 Rank genes for characterizing groups, using `tl.rank_genes_groups`

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1048 ==================================================================

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1049

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1050 It returns:

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1051

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1052 - `Gene names`: Gene names ordered in column by group id and in rows according to scores

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1053 - `Scores`: Score for each gene (rows) for each group (columns), same order as for the names

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1054

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1055 More details on the `scanpy documentation

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1056 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.rank_genes_groups.html#scanpy.api.tl.rank_genes_groups>`__

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1057

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1058 ]]></help>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1059 <expand macro="citations"/>

0e212e42ef88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1060 </tool>

Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

annotate cluster_reduce_dimension.xml @ 0:0e212e42ef88 draft