Mercurial > repos > iuc > scanpy_remove_confounders

annotate remove_confounders.xml @ 0:9ca360dde8e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
author iuc
date Mon, 04 Mar 2019 10:16:47 -0500
parents
children a89ee42625ad
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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1 <tool id="scanpy_remove_confounders" name="Remove confounders with scanpy" version="@version@">
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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2 <description></description>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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3 <macros>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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4 <import>macros.xml</import>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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5 <xml name="score_genes_params">
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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6 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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7 <param argument="random_state" type="integer" value="0" label="Random seed for sampling" help=""/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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8 <expand macro="param_use_raw"/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
iuc
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9 </xml>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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10 <token name="@CMD_score_genes_inputs@"><![CDATA[
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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11 n_bins=$method.n_bins,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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12 random_state=$method.random_state,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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13 use_raw=$method.use_raw,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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14 copy=False
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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15 ]]></token>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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16 </macros>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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17 <expand macro="requirements"/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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18 <command detect_errors="exit_code"><![CDATA[
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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19 @CMD@
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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20 ]]></command>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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21 <configfiles>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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22 <configfile name="script_file"><![CDATA[
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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23 @CMD_imports@
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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24 @CMD_read_inputs@
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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25
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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26 #if $method.method == "pp.regress_out"
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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27 sc.pp.regress_out(
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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28 adata=adata,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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29 keys='$method.reg_keys',
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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30 copy=False)
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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31 #elif $method.method == "tl.score_genes"
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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32 sc.tl.score_genes(
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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33 adata=adata,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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34 #set $gene_list = [str(x.strip()) for x in str($method.gene_list).split(',')]
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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35 gene_list=$gene_list,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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36 ctrl_size=$method.ctrl_size,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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37 score_name='$method.score_name',
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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38 #if $method.gene_pool
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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39 #set $gene_pool = [str(x.strip()) for x in $method.gene_pool.split(',')]
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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40 gene_pool=$gene_pool,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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41 #end if
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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42 @CMD_score_genes_inputs@)
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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43 adata.obs.to_csv('$obs', sep='\t')
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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44 #elif $method.method == "tl.score_genes_cell_cycle"
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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45 sc.tl.score_genes_cell_cycle(
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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46 adata=adata,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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47 #set $s_genes = [str(x.strip()) for x in $method.s_genes.split(',')]
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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48 s_genes=$s_genes,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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49 #set $g2m_genes = [str(x.strip()) for x in $method.g2m_genes.split(',')]
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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50 g2m_genes=$g2m_genes,
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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51 @CMD_score_genes_inputs@)
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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52 adata.obs.to_csv('$obs', sep='\t')
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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53 #end if
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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54
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55 @CMD_anndata_write_outputs@
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56 ]]></configfile>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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57 </configfiles>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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58 <inputs>
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59 <expand macro="inputs_anndata"/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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60 <conditional name="method">
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61 <param argument="method" type="select" label="Method used for plotting">
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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62 <option value="pp.regress_out">Regress out unwanted sources of variation, using `pp.regress_out`</option>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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63 <!--<option value="pp.mnn_correct">, using `pp.mnn_correct`</option>!-->
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64 <!--<option value="pp.dca">, using `pp.mnn_correct`</option>!-->
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65 <!--<option value="pp.magic">, using `pp.magic`</option>!-->
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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66 <!--<option value="tl.sim">, using `tl.sim`</option>!-->
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67 <!--<option value="pp.calculate_qc_metrics">, using `pp.calculate_qc_metrics`</option>!-->
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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68 <option value="tl.score_genes">Score a set of genes, using `tl.score_genes`</option>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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69 <option value="tl.score_genes_cell_cycle">Score cell cycle genes, using `tl.score_genes_cell_cycle`</option>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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70 <!--<option value="tl.cyclone">, using `tl.cyclone`</option>!-->
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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71 <!--<option value="tl.andbag">, using `tl.andbag`</option>!-->
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72 </param>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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73 <when value="pp.regress_out">
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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74 <param argument="reg_keys" type="text" value="" label="Keys for observation annotation on which to regress on" help=""/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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75 </when>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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76 <when value="tl.score_genes">
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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77 <param argument="gene_list" type="text" value="" label="The list of gene names used for score calculation" help="Genes separated by a comma"/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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78 <param argument="ctrl_size" type="integer" value="50" label="Number of reference genes to be sampled"
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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79 help="If `len(gene_list)` is not too low, you can set `ctrl_size=len(gene_list)`."/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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80 <param argument="gene_pool" type="text" value="" optional="true" label="Genes for sampling the reference set"
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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81 help="Default is all genes. Genes separated by a comma"/>
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82 <expand macro="score_genes_params"/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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83 <param argument="score_name" type="text" value="score" label="Name of the field to be added in `.obs`" help=""/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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84 </when>
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85 <when value="tl.score_genes_cell_cycle">
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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86 <param name="s_genes" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma"/>
9ca360dde8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6
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87 <param name="g2m_genes" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma"/>
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88 <expand macro="score_genes_params"/>
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89 </when>
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90 </conditional>
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91 <expand macro="anndata_output_format"/>
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92 </inputs>
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93 <outputs>
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94 <expand macro="anndata_outputs"/>
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95 <data name="obs" format="tabular" label="${tool.name} on ${on_string}: Observations annotation">
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96 <filter>method['method'] == 'tl.score_genes' or method['method'] == 'tl.score_genes_cell_cycle'</filter>
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97 </data>
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98 </outputs>
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99 <tests>
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100 <test>
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101 <conditional name="input">
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102 <param name="format" value="h5ad" />
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103 <param name="adata" value="krumsiek11.h5ad" />
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104 </conditional>
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105 <conditional name="method">
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106 <param name="method" value="pp.regress_out"/>
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107 <param name="reg_keys" value="cell_type"/>
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108 </conditional>
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109 <param name="anndata_output_format" value="h5ad" />
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110 <assert_stdout>
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111 <has_text_matching expression="sc.pp.regress_out"/>
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112 <has_text_matching expression="keys='cell_type'"/>
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113 </assert_stdout>
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114 <output name="anndata_out_h5ad" file="pp.regress_out.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
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115 </test>
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116 <test>
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117 <conditional name="input">
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118 <param name="format" value="h5ad" />
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119 <param name="adata" value="krumsiek11.h5ad" />
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120 </conditional>
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121 <conditional name="method">
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122 <param name="method" value="tl.score_genes"/>
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123 <param name="gene_list" value="Gata2, Fog1"/>
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124 <param name="ctrl_size" value="2"/>
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125 <param name="n_bins" value="2"/>
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126 <param name="random_state" value="2"/>
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127 <param name="use_raw" value="False"/>
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128 <param name="score_name" value="score"/>
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129 </conditional>
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130 <param name="anndata_output_format" value="h5ad"/>
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131 <assert_stdout>
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132 <has_text_matching expression="sc.tl.score_genes" />
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133 <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]" />
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134 <has_text_matching expression="ctrl_size=2" />
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135 <has_text_matching expression="score_name='score'" />
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136 <has_text_matching expression="n_bins=2" />
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137 <has_text_matching expression="random_state=2" />
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138 <has_text_matching expression="use_raw=False" />
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139 <has_text_matching expression="copy=False" />
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140 </assert_stdout>
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141 <output name="anndata_out_h5ad" file="tl.score_genes.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
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142 <output name="obs" file="tl.score_genes.krumsiek11.obs.tabular" ftype="tabular" compare="sim_size"/>
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143 </test>
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144 <test>
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145 <conditional name="input">
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146 <param name="format" value="h5ad" />
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147 <param name="adata" value="krumsiek11.h5ad" />
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148 </conditional>
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149 <conditional name="method">
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150 <param name="method" value="tl.score_genes_cell_cycle"/>
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151 <param name="s_genes" value="Gata2, Fog1, EgrNab"/>
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152 <param name="g2m_genes" value="Gata2, Fog1, EgrNab"/>
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153 <param name="n_bins" value="2"/>
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154 <param name="random_state" value="1"/>
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155 <param name="use_raw" value="False"/>
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156 </conditional>
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157 <param name="anndata_output_format" value="h5ad"/>
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158 <assert_stdout>
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159 <has_text_matching expression="sc.tl.score_genes_cell_cycle"/>
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160 <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/>
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161 <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/>
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162 <has_text_matching expression="n_bins=2"/>
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163 <has_text_matching expression="random_state=1"/>
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164 <has_text_matching expression="use_raw=False"/>
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165 </assert_stdout>
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166 <output name="anndata_out_h5ad" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5" compare="sim_size"/>
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167 <output name="obs" file="tl.score_genes_cell_cycle.krumsiek11.obs.tabular" ftype="tabular" compare="sim_size"/>
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168 </test>
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169 </tests>
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170 <help><![CDATA[
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171 Regress out unwanted sources of variation, using `pp.regress_out`
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172 =================================================================
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173
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174 Regress out unwanted sources of variation, using simple linear regression. This is
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175 inspired by Seurat's `regressOut` function in R.
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176
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177 More details on the `scanpy documentation
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178 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.pp.regress_out.html#scanpy.api.pp.regress_out>`__
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179
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180 Score a set of genes, using `tl.score_genes`
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181 ============================================
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182
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183 The score is the average expression of a set of genes subtracted with the
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184 average expression of a reference set of genes. The reference set is
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185 randomly sampled from the `gene_pool` for each binned expression value.
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186
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187 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented
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188 for Scanpy by Davide Cittaro.
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189
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190 More details on the `scanpy documentation
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191 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.score_genes.html#scanpy.api.tl.score_genes>`__
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192
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193 Score cell cycle genes, using `tl.score_genes_cell_cycle`
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194 =========================================================
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195
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196 Given two lists of genes associated to S phase and G2M phase, calculates
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197 scores and assigns a cell cycle phase (G1, S or G2M). See
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198 `score_genes` for more explanation.
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199
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200 More details on the `scanpy documentation
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201 <https://scanpy.readthedocs.io/en/latest/api/scanpy.api.tl.score_genes_cell_cycle.html#scanpy.api.tl.score_genes_cell_cycle>`__
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202 ]]></help>
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203 <expand macro="citations"/>
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204 </tool>