Mercurial > repos > iuc > scanpy_cluster_reduce_dimension
comparison cluster_reduce_dimension.xml @ 12:6acb08931836 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
| author | iuc |
|---|---|
| date | Fri, 17 Nov 2023 09:13:40 +0000 |
| parents | edec35114f72 |
| children | 6f83f8fd381f |
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| 11:edec35114f72 | 12:6acb08931836 |
|---|---|
| 1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@"> | 1 <tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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 <xml name="pca_inputs"> | 5 <xml name="pca_inputs"> |
| 6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/> | 6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/> |
| 108 copy =False) | 108 copy =False) |
| 109 | 109 |
| 110 #else if $method.method == 'tl.tsne' | 110 #else if $method.method == 'tl.tsne' |
| 111 sc.tl.tsne( | 111 sc.tl.tsne( |
| 112 adata=adata, | 112 adata=adata, |
| 113 #if $method.n_pcs | 113 #if str($method.n_pcs) != '' |
| 114 n_pcs=$method.n_pcs, | 114 n_pcs=$method.n_pcs, |
| 115 #end if | 115 #end if |
| 116 perplexity=$method.perplexity, | 116 perplexity=$method.perplexity, |
| 117 early_exaggeration=$method.early_exaggeration, | 117 early_exaggeration=$method.early_exaggeration, |
| 118 learning_rate=$method.learning_rate, | 118 learning_rate=$method.learning_rate, |
| 124 sc.tl.umap( | 124 sc.tl.umap( |
| 125 adata=adata, | 125 adata=adata, |
| 126 min_dist=$method.min_dist, | 126 min_dist=$method.min_dist, |
| 127 spread=$method.spread, | 127 spread=$method.spread, |
| 128 n_components=$method.n_components, | 128 n_components=$method.n_components, |
| 129 #if $method.maxiter | 129 #if str($method.maxiter) != '' |
| 130 maxiter=$method.maxiter, | 130 maxiter=$method.maxiter, |
| 131 #end if | 131 #end if |
| 132 alpha=$method.alpha, | 132 alpha=$method.alpha, |
| 133 gamma=$method.gamma, | 133 gamma=$method.gamma, |
| 134 negative_sample_rate=$method.negative_sample_rate, | 134 negative_sample_rate=$method.negative_sample_rate, |
| 135 init_pos='$method.init_pos', | 135 init_pos='$method.init_pos', |
| 136 random_state=$method.random_state, | 136 random_state=$method.random_state, |
| 137 copy=False) | 137 copy=False) |
| 138 | 138 |
| 139 #else if $method.method == 'tl.draw_graph' | 139 #else if $method.method == 'tl.draw_graph' |
| 140 | |
| 141 #if str($method.adjacency) != 'None' | 140 #if str($method.adjacency) != 'None' |
| 142 from scipy import io | 141 from scipy import io |
| 143 adjacency = io.mmread('$method.adjacency') | 142 adjacency = io.mmread('$method.adjacency') |
| 144 #end if | 143 #end if |
| 145 | 144 |
| 146 sc.tl.draw_graph( | 145 sc.tl.draw_graph( |
| 147 adata=adata, | 146 adata=adata, |
| 148 layout='$method.layout', | 147 layout='$method.layout', |
| 149 #if str($method.root) != '' | 148 #if $method.root |
| 150 #set $root=([int(x.strip()) for x in str($method.root).split(',')]) | 149 #set $root=([int(x.strip()) for x in str($method.root).split(',')]) |
| 151 root=$root, | 150 root=$root, |
| 152 #end if | 151 #end if |
| 153 random_state=$method.random_state, | 152 random_state=$method.random_state, |
| 154 #if str($method.init_pos) != '' | 153 #if $method.init_pos |
| 155 init_pos='$method.init_pos', | 154 init_pos='$method.init_pos', |
| 156 #end if | 155 #end if |
| 157 #if str($method.adjacency) != 'None' | 156 #if str($method.adjacency) != 'None' |
| 158 adjacency=adjacency, | 157 adjacency=adjacency, |
| 159 #end if | 158 #end if |
| 160 #if str($method.key_ext) != '' | 159 #if $method.key_ext |
| 161 key_ext='$method.key_ext', | 160 key_ext='$method.key_ext', |
| 162 #end if | 161 #end if |
| 163 copy=False) | 162 copy=False) |
| 164 | 163 |
| 165 #else if $method.method == "tl.paga" | 164 #else if $method.method == "tl.paga" |
| 181 | 180 |
| 182 #else if $method.method == "tl.embedding_density" | 181 #else if $method.method == "tl.embedding_density" |
| 183 sc.tl.embedding_density( | 182 sc.tl.embedding_density( |
| 184 adata=adata, | 183 adata=adata, |
| 185 basis='$method.basis', | 184 basis='$method.basis', |
| 186 #if str($method.groupby) != '' | 185 #if $method.groupby |
| 187 groupby='$method.groupby', | 186 groupby='$method.groupby', |
| 188 #end if | 187 #end if |
| 189 #if str($method.key_added) != '' | 188 #if $method.key_added |
| 190 key_added='$method.key_added', | 189 key_added='$method.key_added', |
| 191 #end if | 190 #end if |
| 192 ) | 191 ) |
| 193 | 192 |
| 194 #end if | 193 #end if |