Mercurial > repos > ebi-gxa > seurat_run_umap
annotate seurat_run_umap.xml @ 0:b9424c715a0d draft default tip
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author | ebi-gxa |
---|---|
date | Sat, 02 Mar 2024 10:40:43 +0000 |
parents | |
children |
rev | line source |
---|---|
0
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
1 <tool id="seurat_run_umap" name="Seurat UMAP" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
2 <description>dimensionality reduction</description> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
3 <macros> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
4 <import>seurat_macros.xml</import> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
5 </macros> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
7 <expand macro="version" /> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
8 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
9 <command detect_errors="exit_code"><![CDATA[ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
10 @INPUT_OBJ_PREAMBLE@ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
11 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
12 seurat-run-umap.R |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
13 @INPUT_OBJECT@ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
14 @OUTPUT_OBJECT@ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
15 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
16 #if $dims |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
17 --dims '$dims' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
18 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
19 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
20 #if $reduction |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
21 --reduction '$reduction' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
22 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
23 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
24 #if $adv.graph |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
25 --graph '$adv.graph' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
26 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
27 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
28 #if $assay |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
29 --assay '$assay' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
30 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
31 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
32 #if $adv.nn_name |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
33 --nn.name '$adv.nn_name' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
34 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
35 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
36 #if $adv.slot |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
37 --slot '$adv.slot' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
38 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
39 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
40 #if $adv.umap_method |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
41 --umap.method '$adv.umap_method' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
42 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
43 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
44 #if $adv.reduction_model |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
45 --reduction.model '$adv.reduction_model' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
46 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
47 $adv.return_model |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
48 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
49 #if $n_neighbors |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
50 --n.neighbors '$n_neighbors' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
51 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
52 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
53 #if $n_components |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
54 --n.components '$n_components' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
55 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
56 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
57 #if $adv.metric |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
58 --metric '$adv.metric' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
59 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
60 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
61 #if $adv.n_epochs |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
62 --n.epochs '$adv.n_epochs' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
63 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
64 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
65 #if $adv.learning_rate |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
66 --learning.rate '$adv.learning_rate' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
67 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
68 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
69 #if $adv.min_dist |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
70 --min.dist '$adv.min_dist' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
71 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
72 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
73 #if $adv.spread |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
74 --spread '$adv.spread' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
75 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
76 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
77 #if $local_connectivity |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
78 --local.connectivity '$local_connectivity' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
79 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
80 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
81 #if $adv.repulsion_strength |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
82 --repulsion.strength '$adv.repulsion_strength' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
83 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
84 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
85 #if $adv.negative_sample_rate |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
86 --negative.sample.rate '$adv.negative_sample_rate' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
87 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
88 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
89 #if $adv.a |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
90 --a '$adv.a' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
91 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
92 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
93 #if $adv.b |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
94 --b '$adv.b' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
95 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
96 $adv.uwot_sgd |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
97 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
98 #if $seed_use |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
99 --seed.use '$seed_use' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
100 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
101 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
102 ##if $adv.metric_kwds |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
103 ## --metric.kwds '$adv.metric_kwds' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
104 ##end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
105 $adv.angular_rp_forest |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
106 $adv.verbose |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
107 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
108 #if $reduction_name |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
109 --reduction.name '$reduction_name' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
110 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
111 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
112 #if $reduction_key |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
113 --reduction.key '$reduction_key' |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
114 #end if |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
115 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
116 ]]></command> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
117 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
118 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
119 <inputs> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
120 <expand macro="input_object_params"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
121 <expand macro="output_object_params"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
122 <param label="Dims" optional='true' name="dims" argument="--dims" type="text" help="Which dimensions to use as input features, used only if list('features') is NULL"> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
123 <validator type="regex" message="Value may only include numbers, colon, 'c', commas and parenthesis, to do things such as 1:10 or c(1,2,3).">^[c0-9:,)(]+$</validator> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
124 </param> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
125 <param label="Reduction" optional='true' value='pca' name="reduction" argument="--reduction" type="text" help="Which dimensional reduction (PCA or ICA) to use for the UMAP input. Default is PCA"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
126 <param label="Assay" optional='true' name="assay" argument="--assay" type="text" help="Assay to pull data for when using list('features') , or assay used to construct Graph if running UMAP on a Graph"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
127 <param label="N neighbors" optional='true' value='30' name="n_neighbors" argument="--n.neighbors" type="integer" help="This determines the number of neighboring points used in local approximations of manifold structure. Larger values will result in more global structure being preserved at the loss of detailed local structure. In general this parameter should often be in the range 5 to 50."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
128 <param label="N components" optional='true' value='2' name="n_components" argument="--n.components" type="integer" help="The dimension of the space to embed into."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
129 <param label="Local connectivity" optional='true' value='1' name="local_connectivity" argument="--local.connectivity" type="integer" help="The local connectivity required - i.e. the number of nearest neighbors that should be assumed to be connected at a local level. The higher this value the more connected the manifold becomes locally. In practice this should be not more than the local intrinsic dimension of the manifold."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
130 <param label="Seed use" optional='true' value='42' name="seed_use" argument="--seed.use" type="integer" help="Set a random seed. By default, sets the seed to 42. Setting NULL will not set a seed"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
131 <param label="Reduction name" optional='true' value='umap' name="reduction_name" argument="--reduction.name" type="text" help="Name to store dimensional reduction under in the Seurat object"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
132 <param label="Reduction key" optional='true' value='UMAP' name="reduction_key" argument="--reduction.key" type="text" help="dimensional reduction key, specifies the string before the number for the dimension names. UMAP by default"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
133 <section name="adv" title="Advanced options"> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
134 <param label="Graph" optional='true' name="graph" argument="--graph" type="text" help="Name of graph on which to run UMAP"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
135 <param label="Nn name" optional='true' name="nn_name" argument="--nn.name" type="text" help="Name of knn output on which to run UMAP"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
136 <param label="Slot" optional='true' value='data' name="slot" argument="--slot" type="text" help="The slot used to pull data for when using list('features') . data slot is by default."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
137 <param label="Umap method" optional='true' value='uwot' name="umap_method" argument="--umap.method" type="text" help="UMAP implementation to run. Can be list uwot, uwot-learn, umap-learn (rquires python umap-learn package)."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
138 <param label="Reduction model" optional='true' name="reduction_model" argument="--reduction.model" type="text" help="list('DimReduc') object that contains the umap model"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
139 <param label="Return model" optional='true' value='false' name="return_model" argument="--return.model" type="boolean" truevalue='--return.model' falsevalue='' checked='false' help="whether UMAP will return the uwot model"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
140 <param label="Metric" optional='true' value='cosine' name="metric" argument="--metric" type="text" help="metric: This determines the choice of metric used to measure distance in the input space. A wide variety of metrics are already coded, and a user defined function can be passed as long as it has been JITd by numba."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
141 <param label="N epochs" optional='true' name="n_epochs" argument="--n.epochs" type="integer" help="The number of training epochs to be used in optimizing the low dimensional embedding. Larger values result in more accurate embeddings. If NULL is specified, a value will be selected based on the size of the input dataset (200 for large datasets, 500 for small)."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
142 <param label="Learning rate" optional='true' value='1' name="learning_rate" argument="--learning.rate" type="integer" help="The initial learning rate for the embedding optimization."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
143 <param label="Min dist" optional='true' value='0' name="min_dist" argument="--min.dist" type="integer" help="This controls how tightly the embedding is allowed compress points together. Larger values ensure embedded points are moreevenly distributed, while smaller values allow the algorithm to optimise more accurately with regard to local structure. Sensible values are in the range 0.001 to 0.5."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
144 <param label="Spread" optional='true' value='1' name="spread" argument="--spread" type="integer" help="The effective scale of embedded points. In combination with min.dist this determines how clustered/clumped the embedded points are."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
145 <param label="Repulsion strength" optional='true' value='1' name="repulsion_strength" argument="--repulsion.strength" type="integer" help="Weighting applied to negative samples in low dimensional embedding optimization. Values higher than one will result in greater weight being given to negative samples."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
146 <param label="Negative sample rate" optional='true' value='5' name="negative_sample_rate" argument="--negative.sample.rate" type="integer" help="The number of negative samples to select per positive sample in the optimization process. Increasing this value will result in greater repulsive force being applied, greater optimization cost, but slightly more accuracy."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
147 <param label="A" optional='true' name="a" argument="--a" type="text" help="More specific parameters controlling the embedding. If NULL, these values are set automatically as determined by min. dist and spread. Parameter of differentiable approximation of right adjoint functor."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
148 <param label="B" optional='true' name="b" argument="--b" type="text" help="More specific parameters controlling the embedding. If NULL, these values are set automatically as determined by min. dist and spread. Parameter of differentiable approximation of right adjoint functor."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
149 <param label="Uwot sgd" optional='true' value='false' name="uwot_sgd" argument="--uwot.sgd" type="boolean" truevalue='--uwot.sgd' falsevalue='' checked='false' help="Set list('uwot::umap(fast_sgd = TRUE)') ; see list('umap') for more details"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
150 <!-- Potential injection concern, needs to be handled better before being enabled. |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
151 <param label="Metric kwds" optional='true' name="metric_kwds" argument="metric.kwds" type="text" help="A dictionary of arguments to pass on to the metric, such as the p value for Minkowski distance. If NULL then no arguments are passed on."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
152 --> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
153 <param label="Angular rp forest" optional='true' value='false' name="angular_rp_forest" argument="--angular.rp.forest" type="boolean" truevalue='--angular.rp.forest' falsevalue='' checked='false' help="Whether to use an angular random projection forest to initialise the approximate nearest neighbor search. This can be faster, but is mostly on useful for metric that use an angular style distance such as cosine, correlation etc. In the case of those metrics angular forests will be chosen automatically."/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
154 <param label="Verbose" optional='true' value='true' name="verbose" argument="--do-not-verbose" type="boolean" truevalue='' falsevalue='--do-not-verbose' checked='true' help="Controls verbosity"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
155 </section> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
156 </inputs> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
157 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
158 <outputs> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
159 <expand macro="output_files"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
160 </outputs> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
161 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
162 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
163 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
164 <tests> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
165 <!-- MANUAL TESTS --> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
166 <test> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
167 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-clusters.rds"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
168 <param name="dims" value="1:10"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
169 <output name="rds_seurat_file" ftype="rdata" > |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
170 <assert_contents> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
171 <has_size value="5067150" delta="200000"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
172 </assert_contents> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
173 </output> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
174 </test> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
175 <test> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
176 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-clusters.rds"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
177 <param name="dims" value="c(1,2,3,4,5,6,7,8,9,10)"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
178 <output name="rds_seurat_file" ftype="rdata" > |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
179 <assert_contents> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
180 <has_size value="5067150" delta="200000"/> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
181 </assert_contents> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
182 </output> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
183 </test> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
184 <!-- END MANUAL TESTS --> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
185 </tests> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
186 <help> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
187 <!-- MANUAL HELP --> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
188 <![CDATA[ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
189 .. class:: infomark |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
190 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
191 **What it does** |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
192 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
193 @SEURAT_INTRO@ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
194 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
195 For more details on this method, please see the individual in-line documentation or the same method's Seurat 4 documentation. |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
196 |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
197 @VERSION_HISTORY@ |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
198 ]]> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
199 <!-- END MANUAL HELP --> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
200 </help> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
201 <expand macro="citations" /> |
b9424c715a0d
planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
ebi-gxa
parents:
diff
changeset
|
202 </tool> |