Mercurial > repos > iuc > scanpy_remove_confounders
comparison remove_confounders.xml @ 6:f2f6c703da06 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
| author | iuc |
|---|---|
| date | Thu, 20 Feb 2020 08:24:15 -0500 |
| parents | 524aa62a6066 |
| children | 215733a383f2 |
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| 5:524aa62a6066 | 6:f2f6c703da06 |
|---|---|
| 101 </when> | 101 </when> |
| 102 <when value="pp.combat"> | 102 <when value="pp.combat"> |
| 103 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/> | 103 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/> |
| 104 </when> | 104 </when> |
| 105 </conditional> | 105 </conditional> |
| 106 <expand macro="inputs_common_advanced"/> | |
| 106 </inputs> | 107 </inputs> |
| 107 <outputs> | 108 <outputs> |
| 108 <expand macro="anndata_outputs"/> | 109 <expand macro="anndata_outputs"/> |
| 109 </outputs> | 110 </outputs> |
| 110 <tests> | 111 <tests> |
| 111 <test> | 112 <test> |
| 112 <!-- test 1 --> | 113 <!-- test 0 --> |
| 113 <param name="adata" value="krumsiek11.h5ad" /> | 114 <param name="adata" value="krumsiek11.h5ad" /> |
| 114 <conditional name="method"> | 115 <conditional name="method"> |
| 115 <param name="method" value="pp.regress_out"/> | 116 <param name="method" value="pp.regress_out"/> |
| 116 <param name="keys" value="cell_type"/> | 117 <param name="keys" value="cell_type"/> |
| 117 </conditional> | 118 </conditional> |
| 118 <assert_stdout> | 119 <section name="advanced_common"> |
| 119 <has_text_matching expression="sc.pp.regress_out"/> | 120 <param name="show_log" value="true" /> |
| 120 <has_text_matching expression="keys=\['cell_type'\]"/> | 121 </section> |
| 121 </assert_stdout> | 122 <output name="hidden_output"> |
| 123 <assert_contents> | |
| 124 <has_text_matching expression="sc.pp.regress_out"/> | |
| 125 <has_text_matching expression="keys=\['cell_type'\]"/> | |
| 126 </assert_contents> | |
| 127 </output> | |
| 122 <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> | 128 <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> |
| 123 </test> | 129 </test> |
| 124 <!--<test> | 130 <!--<test> |
| 125 < test 2 > | 131 < test 2 > |
| 126 <param name="adata" value="krumsiek11.h5ad" /> | 132 <param name="adata" value="krumsiek11.h5ad" /> |
| 133 <has_text_matching expression="keys='cell_type'"/> | 139 <has_text_matching expression="keys='cell_type'"/> |
| 134 </assert_stdout> | 140 </assert_stdout> |
| 135 <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> | 141 <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> |
| 136 </test>--> | 142 </test>--> |
| 137 <test> | 143 <test> |
| 138 <!-- test 2 --> | 144 <!-- test 1 --> |
| 139 <param name="adata" value="blobs.h5ad" /> | 145 <param name="adata" value="blobs.h5ad" /> |
| 140 <conditional name="method"> | 146 <conditional name="method"> |
| 141 <param name="method" value="pp.combat"/> | 147 <param name="method" value="pp.combat"/> |
| 142 <param name="key" value="blobs"/> | 148 <param name="key" value="blobs"/> |
| 143 </conditional> | 149 </conditional> |
| 144 <assert_stdout> | 150 <section name="advanced_common"> |
| 145 <has_text_matching expression="sc.pp.combat"/> | 151 <param name="show_log" value="true" /> |
| 146 <has_text_matching expression="key='blobs'"/> | 152 </section> |
| 147 </assert_stdout> | 153 <output name="hidden_output"> |
| 154 <assert_contents> | |
| 155 <has_text_matching expression="sc.pp.combat"/> | |
| 156 <has_text_matching expression="key='blobs'"/> | |
| 157 </assert_contents> | |
| 158 </output> | |
| 148 <output name="anndata_out" file="pp.combat.blobs.h5ad" ftype="h5ad" compare="sim_size"/> | 159 <output name="anndata_out" file="pp.combat.blobs.h5ad" ftype="h5ad" compare="sim_size"/> |
| 149 </test> | 160 </test> |
| 150 </tests> | 161 </tests> |
| 151 <help><![CDATA[ | 162 <help><![CDATA[ |
| 152 Regress out unwanted sources of variation, using `pp.regress_out` | 163 Regress out unwanted sources of variation, using `pp.regress_out` |