Mercurial > repos > iuc > scanpy_remove_confounders
comparison remove_confounders.xml @ 7:215733a383f2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author | iuc |
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date | Wed, 20 May 2020 16:07:23 -0400 |
parents | f2f6c703da06 |
children | bf2017df9837 |
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6:f2f6c703da06 | 7:215733a383f2 |
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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> |