Mercurial > repos > iuc > seurat_reduce_dimension

annotate reduce_dimensions.xml @ 1:46ed93e8da30 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
author iuc
date Tue, 05 Nov 2024 11:55:04 +0000
parents e49429e8d6dd
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e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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1 <tool id="seurat_reduce_dimension" name="Seurat Run Dimensional Reduction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>- PCA, tSNE or UMAP</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1
46ed93e8da30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @CMD@
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="script_file"><![CDATA[
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14 @CMD_imports@
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15 @CMD_read_inputs@
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16
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17 #if $method.method == 'RunPCA'
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19 #if $method.features
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20 features_list<-paste(readLines('$method.features'), collapse=",")
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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21 #end if
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22
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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23 seurat_obj<-RunPCA(
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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24 seurat_obj,
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25 #if $method.assay != ''
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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26 assay = '$method.assay',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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27 #end if
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28 #if $method.features
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29 features = c(unlist(strsplit(features_list, ","))),
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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30 #end if
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31 npcs = $method.npcs,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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32 rev.pca = $method.rev_pca,
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33 weight.by.var = $method.weight_by_var,
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34 reduction.key = '$method.reduction_key',
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35 seed.use = $method.seed_use,
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36 approx = $method.approx,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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37 reduction.name = '$method.reduction_name'
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38 )
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39
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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40 #if $method.print_pcs.print_pcs == 'true'
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41 sink('print_pcs.txt')
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42 print(
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43 seurat_obj[['pca']],
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44 dims = 1:$method.print_pcs.dims,
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45 nfeatures = $method.print_pcs.nfeatures
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46 )
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47 sink()
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48 #end if
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49
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50 #else if $method.method == 'RunTSNE'
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51 seurat_obj<-RunTSNE(
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52 seurat_obj,
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53 #if $method.reduction != ''
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54 reduction = '$method.reduction',
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55 #end if
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56 #if $method.dims
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57 dims = 1:$method.dims,
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58 #end if
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59 #if $method.assay != ''
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60 assay = '$method.assay',
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61 #end if
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62 seed.use = $method.seed_use,
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63 tsne.method = '$method.tsne_method',
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64 dim.embed = $method.dim_embed,
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65 reduction.key = '$method.reduction_key',
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66 reduction.name = '$method.reduction_name'
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67 )
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68
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69 #else if $method.method == 'RunUMAP'
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70 @reticulate_hack@
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71
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72 #if $method.run_umap_on.run_umap_on == 'features'
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73 features_list<-paste(readLines('$method.run_umap_on.features'), collapse=",")
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74 #end if
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75
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76 seurat_obj<-RunUMAP(
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77 seurat_obj,
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78 #if $method.reduction != ''
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79 reduction = '$method.reduction',
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80 #end if
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81 #if $method.assay != ''
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82 assay = '$method.assay',
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83 #end if
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84 reduction.key = '$method.adv.reduction_key',
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85 reduction.name = '$method.adv.reduction_name',
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86 #if $method.adv.reduction_model != ''
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
87 reduction.model = '$method.adv.reduction_model',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
88 #end if
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
89 umap.method ='$method.umap_method.umap_method',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
90 #if $method.umap_method.umap_method == 'umap-learn'
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
91 densmap = $method.umap_method.densmap.densmap,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
92 #if $method.umap_method.densmap.densmap == 'TRUE'
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
93 dens.lambda = $method.umap_method.densmap.dens_lambda,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
94 dens.frac = $method.umap_method.densmap.dens_frac,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
95 dens.var.shift = $method.umap_method.densmap.dens_var_shift,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
96 #end if
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
97 #end if
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
98 n.neighbors = $method.n_neighbors,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
99 n.components = $method.n_components,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
100 metric = '$method.metric',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
101 #if $method.adv.n_epochs
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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102 n.epochs = $method.adv.n_epochs,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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103 #end if
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
104 learning.rate = $method.adv.learning_rate,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
105 min.dist = $method.adv.min_dist,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
106 spread = $method.adv.spread,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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107 set.op.mix.ratio = $method.adv.set_op_mix_ratio,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
108 local.connectivity = $method.adv.local_connectivity,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
109 repulsion.strength = $method.adv.repulsion_strength,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
110 negative.sample.rate = $method.adv.negative_sample_rate,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
111 #if $method.adv.a != ''
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
112 a = '$method.adv.a',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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113 #end if
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
114 #if $method.adv.b != ''
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
115 b = '$method.adv.b',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
116 #end if
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
117 uwot.sgd = $method.adv.uwot_sgd,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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118 seed.use = $method.adv.seed_use,
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iuc
parents:
diff changeset
119 angular.rp.forest = $method.adv.angular_rp_forest,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
120 #if $method.run_umap_on.run_umap_on == 'dims'
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iuc
parents:
diff changeset
121 dims = 1:$method.run_umap_on.dims,
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
122 #else if $method.run_umap_on.run_umap_on == 'features'
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iuc
parents:
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123 features = c(unlist(strsplit(features_list, ","))),
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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124 slot = '$method.run_umap_on.slot',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
125 #else if $method.run_umap_on.run_umap_on == 'graph'
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iuc
parents:
diff changeset
126 graph = '$method.run_umap_on.graph',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
127 #else if $method.run_umap_on.run_umap_on == 'nn_name'
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iuc
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diff changeset
128 nn.names = '$method.run_umap_on.nn_name',
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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129 #end if
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iuc
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130 )
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iuc
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diff changeset
131
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iuc
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diff changeset
132 #end if
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133
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iuc
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134 @CMD_rds_write_outputs@
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iuc
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135
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iuc
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diff changeset
136 ]]></configfile>
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iuc
parents:
diff changeset
137 </configfiles>
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iuc
parents:
diff changeset
138 <inputs>
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iuc
parents:
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139 <expand macro="input_rds"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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140 <conditional name="method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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141 <param name="method" type="select" label="Method used">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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142 <option value="RunPCA">Run a PCA dimensionality reduction using 'RunPCA'</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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143 <option value="RunTSNE">Run a t-SNE dimensionality reduction using 'RunTSNE'</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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144 <option value="RunUMAP">Run a UMAP dimensional reduction using 'RunUMAP'</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
145 </param>
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iuc
parents:
diff changeset
146 <when value="RunPCA">
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iuc
parents:
diff changeset
147 <expand macro="select_assay"/>
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iuc
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148 <param argument="npcs" type="integer" value="50" label="Number of PCs to compute"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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149 <param name="rev_pca" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Compute the PCA on the 'gene x cell' matrix instead of 'cell x gene' matrix" help="(rev.pca)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
150 <param name="weight_by_var" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the cell embeddings by the variance of each PC" help="(weight.by.var)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
151 <param name="seed_use" type="integer" value="42" label="Set a random seed" help="(seed.use)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
152 <param argument="approx" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use truncated singular value decomposition to approximate PCA"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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153 <param argument="features" type="data" format="txt,tabular" optional="true" label="List of features to compute PCA on" help="text file with one feature on each line, default is variable features"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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154 <param name="reduction_name" type="text" value="pca" label="Name for dimensional reduction" help="(reduction.name)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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155 <expand macro="valid_name"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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156 </param>
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iuc
parents:
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157 <param name="reduction_key" type="text" value="PC_" label="Dimensional reduction key" help="specifies the string before the number for the dimension names (reduction.key)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
158 <expand macro="valid_reduction_key"/>
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iuc
parents:
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159 </param>
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iuc
parents:
diff changeset
160 <conditional name="print_pcs">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
161 <param name="print_pcs" type="select" label="Output list of top genes">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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162 <option value="false" selected="true">No</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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163 <option value="true">Yes</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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164 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
165 <when value="false">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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166 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
167 <when value="true">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
168 <param argument="dims" type="integer" value="5" label="Number of PCs to print genes for"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
169 <param argument="nfeatures" type="integer" value="5" label="Number of top genes to print for each PC"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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170 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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171 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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172 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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173 <when value="RunTSNE">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
174 <expand macro="select_reduction_pca"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
175 <expand macro="set_dims"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
176 <expand macro="select_assay"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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177 <param name="tsne_method" type="select" label="Select the method to use to compute the tSNE" help="(tsne.method)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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178 <option value="Rtsne" selected="true">Rtsne</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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179 <option value="FIt-SNE">FIt-SNE</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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180 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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181 <param name="seed_use" type="integer" value="1" label="Set a random seed" help="(seed.use)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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182 <param name="dim_embed" type="integer" value="2" label="Set the dimensional space of the tSNE embedding" help="(dim.embed)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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183 <param name="reduction_name" type="text" value="tsne" label="Name for dimensional reduction" help="(reduction.name)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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diff changeset
184 <expand macro="valid_name"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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185 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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186 <param name="reduction_key" type="text" value="tSNE_" label="Dimensional reduction key" help="specifies the string before the number for the dimension names (reduction.key)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
187 <expand macro="valid_reduction_key"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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188 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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189 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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190 <when value="RunUMAP">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
191 <expand macro="select_reduction_pca"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
192 <expand macro="select_assay"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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193 <conditional name="umap_method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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194 <param name="umap_method" type="select" label="UMAP implementation to run" help="(umap.method)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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195 <option value="uwot" selected="true">uwot</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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196 <option value="uwot-learn">uwot-learn</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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197 <option value="umap-learn">umap-learn</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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198 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
199 <when value="uwot">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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200 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
201 <when value="uwot-learn">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
202 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
203 <when value="umap-learn">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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204 <conditional name="densmap">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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205 <param argument="densmap" type="select" label="Use the density-augmented objective of densMAP">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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206 <option value="TRUE">Yes</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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207 <option value="FALSE" selected="true">No</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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208 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
209 <when value="TRUE">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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210 <param name="dens_lambda" type="integer" optional="true" value="2" label="Control the regularization weight of densMAP density correlation term" help="(dens.lambda)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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211 <param name="dens_frac" type="float" optional="true" min="0" max="1" value="0.3" label="Control the fraction of epochs where density-augmented objective is used in densMAP" help="(dens.frac)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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212 <param name="dens_var_shift" type="float" optional="true" value="0.1" label="Constant to add to variance of local radii when calculating density correlation objective" help="(dens.var.shift)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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213 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
214 <when value="FALSE">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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215 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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216 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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217 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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218 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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219 <param name="n_neighbors" type="integer" value="30" label="Number of neighbors to use" help="Usually in range 5-50 (n.neighbors)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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220 <param name="n_components" type="integer" value="2" label="Dimension of the space to embed into" help="(n.components)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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221 <param argument="metric" type="select" label="Choose metric to use to measure distances in the input space">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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222 <option value="cosine" selected="true">cosine</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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223 <option value="correlation">correlation</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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224 <option value="euclidean">euclidean</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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225 <option value="manhattan">manhattan</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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226 <option value="hamming">hamming</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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227 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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228 <conditional name="run_umap_on">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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229 <param name="run_umap_on" type="select" label="Run UMAP on dimensions, features, graph or KNN output">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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230 <option value="dims" selected="true">dims</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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231 <option value="features">features</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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232 <option value="graph">graph</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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233 <option value="nn_name">nn.name</option>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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234 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
235 <when value="dims">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
236 <expand macro="set_dims"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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237 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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238 <when value="features">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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239 <param argument="features" type="data" format="txt,tabular" optional="true" label="Run UMAP on this subset of features" help="text file with one feature on each line"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
240 <expand macro="select_slot_data"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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241 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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242 <when value="graph">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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243 <param argument="graph" type="text" optional="true" value="" label="Name of graph on which to run UMAP">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
244 <expand macro="valid_name"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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245 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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246 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
247 <when value="nn_name">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
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248 <param name="nn_name" type="text" optional="true" value="" label="Name of KNN output on which to run UMAP" help="(nn.name)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
249 <expand macro="valid_name"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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250 </param>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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251 </when>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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252 </conditional>
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253 <section name="adv" title="Advanced Options">
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254 <param name="reduction_model" type="text" optional="true" value="" label="DimReduct object that contains the umap model" help="(reduction.model)"/>
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255 <param name="n_epochs" type="integer" optional="true" value="" label="Set the number of training epochs to use to optimise the embedding" help="if left empty, will be set as 500 for small datasets, 200 for large datasets (n.epochs)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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256 <param name="learning_rate" type="integer" value="1" label="Initial learning rate for the embedding optimization" help="(learning.rate)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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257 <param name="min_dist" type="float" value="0.3" label="Control how tightly points are compressed in the embedding" help="sensible values are in the range 0.001 to 0.5 (min.dist)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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258 <param argument="spread" type="integer" value="1" label="Effective spread of embedded points"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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259 <param name="set_op_mix_ratio" type="float" value="1.0" label="Interpolate between fuzzy union and intersection" help="(set.op.mix.ratio)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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260 <param name="local_connectivity" type="integer" value="1" label="Set local connectivity" help="the number of nearest neighbors assummed to connect at local level (local.connectivity)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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261 <param name="repulsion_strength" type="integer" value="1" label="Apply weighting to negative values" help="(repulsion.strength)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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262 <param name="negative_sample_rate" type="integer" value="5" label="Number of negative samples to select per positive sample during optimization" help="(negative.sample.rate)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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263 <param argument="a" type="text" optional="true" value="" label="Parameter 'a' of differentiable approximation of right adjoint functor" help="automatically set if left empty"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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264 <param argument="b" type="text" optional="true" value="" label="Parameter 'b' of differentiable approximation of right adjoint functor" help="automatically set if left empty"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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265 <param name="uwot_sgd" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked ="false" label="Set uwot::umap(fast_sgd = TRUE)" help="(uwot.sgd)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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266 <param name="seed_use" type="integer" value="42" label="Set a random seed" help="(seed.use)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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267 <param name="angular_rp_forest" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Use an angular random projection forest to initialise nearest neighbors" help="(angular.rp.forest)"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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268 <param name="reduction_name" type="text" value="umap" label="Name for dimensional reduction" help="(reduction.name)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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269 <expand macro="valid_name"/>
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270 </param>
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271 <param name="reduction_key" type="text" value="UMAP_" label="Dimensional reduction key" help="specifies the string before the number for the dimension names (reduction.key)">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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272 <expand macro="valid_reduction_key"/>
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273 </param>
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274 </section>
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275 </when>
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276 </conditional>
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277 <expand macro="inputs_common_advanced"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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278 </inputs>
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279 <outputs>
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280 <expand macro="seurat_outputs"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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281 <expand macro="print_top_pcs"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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282 </outputs>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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283 <tests>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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284 <test expect_num_outputs="3">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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285 <!-- test1: RunPCA -->
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286 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/scaled.rds"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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287 <conditional name="method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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288 <param name="method" value="RunPCA"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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289 <conditional name="print_pcs">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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290 <param name="print_pcs" value="true"/>
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291 </conditional>
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292 </conditional>
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293 <section name="advanced_common">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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294 <param name="show_log" value="true"/>
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295 </section>
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296 <output name="hidden_output">
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297 <assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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298 <has_text_matching expression="RunPCA"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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299 </assert_contents>
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300 </output>
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301 <output name="rds_out" location="https://zenodo.org/records/13732784/files/pca.rds" ftype="rds" compare="sim_size"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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302 <output name="top_pcs" location="https://zenodo.org/records/13732784/files/top_pcs.txt" ftype="txt">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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303 <assert_contents>
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304 <has_text_matching expression="PC_" n="5"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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305 </assert_contents>
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306 </output>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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307 </test>
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308 <test expect_num_outputs="2">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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309 <!-- test2: RuntSNE -->
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310 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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311 <conditional name="method">
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312 <param name="method" value="RunTSNE"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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313 <param name="seed.use" value="1"/>
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314 <param name="tsne_method" value="Rtsne"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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315 <param name="dim_embed" value="2"/>
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316 <param name="reduction_key" value="tSNE_"/>
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317 </conditional>
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318 <section name="advanced_common">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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319 <param name="show_log" value="true"/>
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320 </section>
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321 <output name="hidden_output">
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322 <assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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323 <has_text_matching expression="RunTSNE"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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324 </assert_contents>
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325 </output>
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326 <output name="rds_out" location="https://zenodo.org/records/13732784/files/tSNE.rds" ftype="rds" compare="sim_size"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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327 </test>
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328 <test expect_num_outputs="2">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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329 <!-- test3: RuntSNE with FIt-SNE -->
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330 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
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331 <conditional name="method">
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332 <param name="method" value="RunTSNE"/>
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333 <param name="seed.use" value="1"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
334 <param name="tsne_method" value="FIt-SNE"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
335 <param name="dim_embed" value="2"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
336 <param name="reduction_key" value="tSNE_"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
337 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
338 <section name="advanced_common">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
339 <param name="show_log" value="true"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
340 </section>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
341 <output name="hidden_output">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
342 <assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
343 <has_text_matching expression="RunTSNE"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
344 </assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
345 </output>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
346 <output name="rds_out" location="https://zenodo.org/records/13732784/files/FIt-SNE.rds" ftype="rds" compare="sim_size"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
347 </test>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
348 <test expect_num_outputs="2">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
349 <!-- test4: RunUMAP -->
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
350 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
351 <conditional name="method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
352 <param name="method" value="RunUMAP"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
353 <param name="reduction_key" value="UMAP_"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
354 <conditional name="umap_method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
355 <param name="umap_method" value="uwot"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
356 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
357 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
358 <section name="advanced_common">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
359 <param name="show_log" value="true"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
360 </section>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
361 <output name="hidden_output">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
362 <assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
363 <has_text_matching expression="RunUMAP"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
364 </assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
365 </output>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
366 <output name="rds_out" location="https://zenodo.org/records/13732784/files/umap.rds" ftype="rds" compare="sim_size"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
367 </test>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
368 <test expect_num_outputs="2">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
369 <!-- test5: RunUMAP - umap-learn -->
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
370 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
371 <conditional name="method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
372 <param name="method" value="RunUMAP"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
373 <param name="reduction_key" value="UMAP_"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
374 <conditional name="umap_method">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
375 <param name="umap_method" value="umap-learn"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
376 <conditional name="densmap">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
377 <param name="densmap" value="FALSE"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
378 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
379 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
380 </conditional>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
381 <section name="advanced_common">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
382 <param name="show_log" value="true"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
383 </section>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
384 <output name="hidden_output">
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
385 <assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
386 <has_text_matching expression="RunUMAP"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
387 </assert_contents>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
388 </output>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
389 <output name="rds_out" location="https://zenodo.org/records/13732784/files/umap-learn.rds" ftype="rds" compare="sim_size"/>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
390 </test>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
391 </tests>
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
392 <help><![CDATA[
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
393 Seurat
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
394 ======
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
395
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
396 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
397
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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diff changeset
398 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
399
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
400 RunPCA
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
401 ======
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
402
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
403 Run a PCA dimensionality reduction.
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
404
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
405 More details on the `seurat documentation
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
406 <https://satijalab.org/seurat/reference/runpca>`__
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
407
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
408 RuntSNE
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
409 =======
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
410
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
411 Run t-SNE dimensionality reduction on selected features.
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
412
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
413 More details on the `seurat documentation
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
414 <https://satijalab.org/seurat/reference/runtsne>`__
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
415
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
416 RunUMAP
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
417 =======
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
418
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
parents:
diff changeset
419 Runs the Uniform Manifold Approximation and Projection (UMAP) dimensional reduction technique.
e49429e8d6dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
iuc
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420
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421 More details on the `seurat documentation
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422 <https://satijalab.org/seurat/reference/runumap>`__
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423
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424 ]]></help>
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425 <expand macro="citations"/>
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426 </tool>