Mercurial > repos > iuc > scanpy_remove_confounders

comparison remove_confounders.xml @ 7:0bea15e9a22d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author iuc
date Wed, 20 May 2020 12:17:20 +0000
parents c0fab89336d1
children daa329d0ee55
comparison
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6:c0fab89336d1 7:0bea15e9a22d
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 <expand macro="sanitize_query" />
77 </param>
76 </when> 78 </when>
77 <when value="pp.mnn_correct"> 79 <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."/> 80 <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"/> 81 <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"/> 82 <expand macro="sanitize_query" />
83 </param>
84 <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate">
85 <expand macro="sanitize_query" />
86 </param>
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"> 87 <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> 88 <option value="-">-</option>
83 <option value="_">_</option> 89 <option value="_">_</option>
84 <option value=" "> </option> 90 <option value=" "> </option>
85 <option value="/">/</option> 91 <option value="/">/</option>
86 </param> 92 </param>
87 <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key"/> 93 <param argument="batch_categories" type="text" value="" optional="true" label="Batch categories for the concatenate" help="List of comma-separated key">
94 <expand macro="sanitize_query" />
95 </param>
88 <param argument="k" type="integer" value="20" label="Number of mutual nearest neighbors"/> 96 <param argument="k" type="integer" value="20" label="Number of mutual nearest neighbors"/>
89 <param argument="sigma" type="float" value="1" label="The bandwidth of the Gaussian smoothing kernel used to compute the correction vectors"/> 97 <param argument="sigma" type="float" value="1" label="The bandwidth of the Gaussian smoothing kernel used to compute the correction vectors"/>
90 <param argument="cos_norm_in" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed on the input data prior to calculating distances between cells?"/> 98 <param argument="cos_norm_in" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed on the input data prior to calculating distances between cells?"/>
91 <param argument="cos_norm_out" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed prior to computing corrected expression values?"/> 99 <param argument="cos_norm_out" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should cosine normalization be performed prior to computing corrected expression values?"/>
92 <param argument="svd_dim" type="integer" value="" optional="true" label="Number of dimensions to use for summarizing biological substructure within each batch" help="If not set, biological components will not be removed from the correction vectors."/> 100 <param argument="svd_dim" type="integer" value="" optional="true" label="Number of dimensions to use for summarizing biological substructure within each batch" help="If not set, biological components will not be removed from the correction vectors."/>
93 <param argument="var_adj" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Adjust variance of the correction vectors?" help="This step takes most computing time."/> 101 <param argument="var_adj" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Adjust variance of the correction vectors?" help="This step takes most computing time."/>
94 <param argument="compute_angle" type="boolean" truevalue="True" falsevalue="False" checked="false" label="compute the angle between each cell’s correction vector and the biological subspace of the reference batch?"/> 102 <param argument="compute_angle" type="boolean" truevalue="True" falsevalue="False" checked="false" label="compute the angle between each cell’s correction vector and the biological subspace of the reference batch?"/>
95 <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially"/> 103 <param argument="mnn_order" type="text" value="" optional="true" label="The order in which batches are to be corrected" help="List of comma-separated key. If not set, datas are corrected sequentially">
104 <expand macro="sanitize_query" />
105 </param>
96 <param name="svd_mode" type="select" label="SVD mode"> 106 <param name="svd_mode" type="select" label="SVD mode">
97 <option value="svd">svd: SVD using a non-randomized SVD-via-ID algorithm</option> 107 <option value="svd">svd: SVD using a non-randomized SVD-via-ID algorithm</option>
98 <option value="rsvd" selected="true">rsvd: SVD using a randomized SVD-via-ID algorithm</option> 108 <option value="rsvd" selected="true">rsvd: SVD using a randomized SVD-via-ID algorithm</option>
99 <option value="irlb">irlb: truncated SVD by implicitly restarted Lanczos bidiagonalization</option> 109 <option value="irlb">irlb: truncated SVD by implicitly restarted Lanczos bidiagonalization</option>
100 </param> 110 </param>
101 </when> 111 </when>
102 <when value="pp.combat"> 112 <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"/> 113 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal">
114 <expand macro="sanitize_query" />
115 </param>
104 </when> 116 </when>
105 </conditional> 117 </conditional>
106 <expand macro="inputs_common_advanced"/> 118 <expand macro="inputs_common_advanced"/>
107 </inputs> 119 </inputs>
108 <outputs> 120 <outputs>