Mercurial > repos > iuc > scanpy_remove_confounders

comparison remove_confounders.xml @ 3:5a97db811365 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
author iuc
date Thu, 12 Dec 2019 14:19:38 +0000
parents c3d6446f0dd2
children e5fa012d8d93
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2:c3d6446f0dd2 3:5a97db811365
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>