Mercurial > repos > iuc > scanpy_remove_confounders
comparison remove_confounders.xml @ 3:00305dc2dd6f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
author | iuc |
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date | Thu, 12 Dec 2019 09:26:22 -0500 |
parents | 94c8f42efc47 |
children | 524aa62a6066 |
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2:94c8f42efc47 | 3:00305dc2dd6f |
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1 <tool id="scanpy_remove_confounders" name="Remove confounders" version="@version@" profile="@profile@"> | 1 <tool id="scanpy_remove_confounders" name="Remove confounders" version="@galaxy_version@" profile="@profile@"> |
2 <description>with scanpy</description> | 2 <description>with scanpy</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
65 </configfiles> | 65 </configfiles> |
66 <inputs> | 66 <inputs> |
67 <expand macro="inputs_anndata"/> | 67 <expand macro="inputs_anndata"/> |
68 <conditional name="method"> | 68 <conditional name="method"> |
69 <param argument="method" type="select" label="Method used for plotting"> | 69 <param argument="method" type="select" label="Method used for plotting"> |
70 <option value="pp.regress_out">Regress out unwanted sources of variation, using `pp.regress_out`</option> | 70 <option value="pp.regress_out">Regress out unwanted sources of variation, using 'pp.regress_out'</option> |
71 <option value="pp.mnn_correct">Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct`</option> | 71 <option value="pp.mnn_correct">Correct batch effects by matching mutual nearest neighbors, using 'pp.mnn_correct'</option> |
72 <option value="pp.combat">Correct batch effects with ComBat function, using `pp.combat`</option> | 72 <option value="pp.combat">Correct batch effects with ComBat function, using 'pp.combat'</option> |
73 </param> | 73 </param> |
74 <when value="pp.regress_out"> | 74 <when value="pp.regress_out"> |
75 <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma"/> | 75 <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma"/> |
76 </when> | 76 </when> |
77 <when value="pp.mnn_correct"> | 77 <when value="pp.mnn_correct"> |
78 <param name="extra_adata" type="data" multiple="true" optional="true" format="h5ad" label="Extra annotated data matrix" help="They should have same number of variables."/> | 78 <param name="extra_adata" type="data" multiple="true" optional="true" format="h5ad" label="Extra annotated data matrix" help="They should have same number of variables."/> |
79 <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from `.var_names`. If not set, all vars are used"/> | 79 <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used"/> |
80 <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate"/> | 80 <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate"/> |
81 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices"> | 81 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices"> |
82 <option value="-">-</option> | 82 <option value="-">-</option> |
83 <option value="_">_</option> | 83 <option value="_">_</option> |
84 <option value=" "> </option> | 84 <option value=" "> </option> |