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annotate cosg.xml @ 0:9d7ccdb258df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
author iuc
date Wed, 29 May 2024 14:25:02 +0000
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children 527d9c6962b0
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9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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1 <tool id="cosg" name="COSG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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2 <description>Cell marker gene identification</description>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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3 <macros>
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4 <import>macros.xml</import>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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5 </macros>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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6 <expand macro="requirements">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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7 </expand>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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8 <expand macro="version_command"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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9 <command detect_errors="exit_code"><![CDATA[
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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10 @CMD@
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11 ]]></command>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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12 <configfiles>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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13 <configfile name="script_file"><![CDATA[
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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14 @CMD_imports@
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15 @CMD_read_inputs@
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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16
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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17 #if $method_options.groups != 'all'
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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18 #set $method_options.groups=[$groups]
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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19 #end if
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20
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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21 cosg.cosg(adata,
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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22 groupby='$method_options.groupby',
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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23 groups='$method_options.groups',
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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24 n_genes_user=$method_options.n_genes_user,
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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25 mu=$advanced_options.mu,
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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26 remove_lowly_expressed=$advanced_options.filter_expression.remove_lowly_expressed,
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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27 #if $advanced_options.filter_expression.remove_lowly_expressed == "True"
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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28 expressed_pct=$advanced_options.filter_expression.expressed_pct,
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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29 #end ifs
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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30 key_added='$advanced_options.key_added',
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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31 use_raw=$advanced_options.layer_selection.use_raw,
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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32 #if $advanced_options.layer_selection.use_raw == "False"
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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33 #if $advanced_options.layer_selection.layer
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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34 layer='$advanced_options.layer_selection.layer',
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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35 #end if
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36 #end if
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37 reference='$advanced_options.reference'
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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38 )
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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39
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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40 df=pd.DataFrame(adata.uns['cosg']['names']).T
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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41 df.to_csv('marker.tsv', sep='\t', index=True)
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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42
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43 @CMD_anndata_write_outputs@
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44 ]]></configfile>
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45 </configfiles>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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46 <inputs>
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47 <expand macro="inputs_anndata"/>
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48 <section name="method_options" title="Method Options" expanded="true">
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49 <param argument="groupby" type="text" value="" optional="false" label="The key of the cell groups in .obs"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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50 <param argument="groups" type="text" value="all" optional="false" label="Subset of cell groups" help="e.g. 'g1','g2','g3'."/>
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51 <param argument="n_genes_user" type="integer" value="50" min="1" label="The number of genes that appear in the returned tables"/>
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52 </section>
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53 <section name="advanced_options" title="Advanced Options">
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54 <param argument="mu" type="float" value="1.0" min="0.0" max="1.0" label="The penalty restricting marker genes expressing in non-target cell groups" help="Larger value represents more strict restrictions. mu should be >= 0, and by default, mu = 1."/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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55 <conditional name="filter_expression">
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56 <param name="remove_lowly_expressed" type="select" label="Remove lowly expressed genes" help="If yes, genes that express a percentage of target cells smaller than a specific value (`expressed_pct`) are not considered as marker genes for the target cells.">
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57 <option value="False">No</option>
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58 <option value="True">Yes</option>
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59 </param>
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60 <when value="False"/>
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61 <when value="True">
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62 <param argument="expressed_pct" type="float" value="0.1" min="0.01" max="1.0" label="Percentage of target cells" help="Genes that express a percentage of target cells smaller than a specific value (`expressed_pct`) are not considered as marker genes for the target cells."/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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63 </when>
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64 </conditional>
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65 <param argument="key_added" type="text" value="cosg" optional="false" label="The key in adata.uns information is saved to.">
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66 <validator type="empty_field"/>
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67 </param>
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68 <conditional name="layer_selection">
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69 <param name="use_raw" type="select" label="Use raw attribute of adata if present to perform tests on." help="If use_raw is set to True then adata.raw.X if it exists.">
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70 <option value="False">No</option>
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71 <option value="True">Yes</option>
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72 </param>
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73 <when value="False">
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74 <param argument="layer" type="text" value="" label="Key from adata.layers whose value will be used to perform tests on." help="If empty then adata.X will be used. If use_raw is set to True then adata.raw.X. If layers specified then use adata.layers[layer]."/>
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75 </when>
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76 <when value="True"/>
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77 </conditional>
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78 <param argument="reference" type="text" value="rest" optional="false" label="If a group identifier, compare with respect to this group." help=" If you use the keyword 'rest', compare each group to the union of the rest of the group.">
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79 <validator type="empty_field"/>
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80 </param>
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81 </section>
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82 <expand macro="inputs_common_advanced"/>
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83 </inputs>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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84 <outputs>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
85 <expand macro="anndata_outputs"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
86 <data name="marker_out" format="tabular" from_work_dir="marker.tsv" label="${tool.name} on ${on_string}: Markers"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
87 </outputs>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
88 <tests>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
89 <test expect_num_outputs="3">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
90 <!-- test 1 -->
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
91 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
92 <param name="groupby" value="bulk_labels"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
93 <section name="advanced_common">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
94 <param name="show_log" value="true" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
95 </section>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
96 <output name="hidden_output">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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97 <assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
98 <has_text_matching expression="cosg.cosg"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
99 <has_text_matching expression="groupby='bulk_labels'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
100 <has_text_matching expression="groups='all'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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101 <has_text_matching expression="n_genes_user=50"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
102 <has_text_matching expression="mu=1.0"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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103 <has_text_matching expression="remove_lowly_expressed=False"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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104 <has_text_matching expression="key_added='cosg'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
105 <has_text_matching expression="use_raw=False"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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106 <has_text_matching expression="reference='rest'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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107 </assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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108 </output>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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109 <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" ftype="h5ad">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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110 <assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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111 <has_h5_keys keys="obs, var, uns" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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112 </assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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113 </output>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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114 <output name="marker_out" file="marker_1.tsv" ftype="tabular" compare="sim_size">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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115 <assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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116 <has_n_columns n="51" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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117 </assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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118 </output>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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119 </test>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
120 <test expect_num_outputs="3">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
121 <!-- test 2 -->
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
122 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
123 <param name="groupby" value="louvain"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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124 <param name="remove_lowly_expressed" value="True" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
125 <section name="advanced_common">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
126 <param name="show_log" value="true" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
127 </section>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
128 <output name="hidden_output">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
129 <assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
130 <has_text_matching expression="cosg.cosg"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
131 <has_text_matching expression="groupby='louvain'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
132 <has_text_matching expression="groups='all'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
133 <has_text_matching expression="n_genes_user=50"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
134 <has_text_matching expression="mu=1.0"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
135 <has_text_matching expression="remove_lowly_expressed=True"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
136 <has_text_matching expression="expressed_pct=0.1"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
137 <has_text_matching expression="key_added='cosg'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
138 <has_text_matching expression="use_raw=False"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
139 <has_text_matching expression="reference='rest'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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diff changeset
140 </assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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diff changeset
141 </output>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
142 <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_2.h5ad" ftype="h5ad">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
143 <assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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144 <has_h5_keys keys="obs, var, uns" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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145 </assert_contents>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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146 </output>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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147 <output name="marker_out" file="marker_2.tsv" ftype="tabular">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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148 <assert_contents>
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iuc
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diff changeset
149 <has_n_columns n="51" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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150 </assert_contents>
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151 </output>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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152 </test>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
153 <test expect_num_outputs="3">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
154 <!-- test 3 -->
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
155 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced.h5ad" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
156 <param name="groupby" value="bulk_labels"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
157 <param name="use_raw" value="True"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
158 <section name="advanced_common">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
159 <param name="show_log" value="true" />
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
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diff changeset
160 </section>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
161 <output name="hidden_output">
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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diff changeset
162 <assert_contents>
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iuc
parents:
diff changeset
163 <has_text_matching expression="cosg.cosg"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
164 <has_text_matching expression="groupby='bulk_labels'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
165 <has_text_matching expression="groups='all'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
166 <has_text_matching expression="n_genes_user=50"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
167 <has_text_matching expression="mu=1.0"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
168 <has_text_matching expression="remove_lowly_expressed=False"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
parents:
diff changeset
169 <has_text_matching expression="key_added='cosg'"/>
9d7ccdb258df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
iuc
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170 <has_text_matching expression="use_raw=True"/>
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171 <has_text_matching expression="reference='rest'"/>
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172 </assert_contents>
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173 </output>
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174 <output name="anndata_out" file="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_3.h5ad" ftype="h5ad">
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175 <assert_contents>
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176 <has_h5_keys keys="obs, var, uns" />
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177 </assert_contents>
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178 </output>
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179 <output name="marker_out" file="marker_3.tsv" ftype="tabular">
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180 <assert_contents>
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181 <has_n_columns n="51" />
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182 </assert_contents>
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183 </output>
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184 </test>
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185 </tests>
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186 <help><![CDATA[
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187 Marker gene identification for single-cell sequencing data using COSG.
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188 ============================================================================================================
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189
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190 Accurate and fast cell marker gene identification with COSG
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191
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192 COSG is a cosine similarity-based method for more accurate and scalable marker gene identification.
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193
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194 - COSG is a general method for cell marker gene identification across different data modalities, e.g., scRNA-seq, scATAC-seq and spatially resolved transcriptome data.
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195 - Marker genes or genomic regions identified by COSG are more indicative and with greater cell-type specificity.
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196 - COSG is ultrafast for large-scale datasets, and is capable of identifying marker genes for one million cells in less than two minutes.
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197
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198 Here is the R version for COSG, and the Python version is hosted in https://github.com/genecell/COSG.
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199
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200 ]]></help>
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201 <expand macro="citations"/>
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202 </tool>