annotate seurat_run_tsne.xml @ 6:0db997e4a81d draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:58 +0000
parents 8d9ceaec2c7f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
1 <tool id="seurat_run_tsne" name="Seurat RunTSNE" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
2 <description>run t-SNE dimensionality reduction</description>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
3 <macros>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
4 <import>seurat_macros.xml</import>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
5 </macros>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
7 <expand macro="version" />
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
9 seurat-run-tsne.R
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
10
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
11 @INPUT_OBJECT@
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
12 #if $genes_use:
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
13 --genes-use '$genes_use'
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
14 #end if
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
15
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
16 #if str($adv.dims_use):
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
17 --dims-use \$(seq -s , 1 '$adv.dims_use')
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
18 #else
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
19 --dims-use 1,10
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
20 #end if
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
21
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
22 #if not $adv.do_fast:
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
23 --do-fast '$adv.do_fast'
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
24 #end if
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
25 #if $adv.tsne_method
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
26 --tsne-method '$adv.tsne_method'
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
27 #end if
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
28 #if $adv.dim_embed
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
29 --dim_embed '$adv.dim_embed'
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
30 #end if
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
31 #if $adv.random_seed
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
32 --random-seed '$adv.random_seed'
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
33 #end if
2
fd0fc93b3c87 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
34 #if $adv.perplexity
fd0fc93b3c87 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
35 --perplexity '$adv.perplexity'
fd0fc93b3c87 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
36 #end if
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
37
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
38 @OUTPUT_OBJECT@
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
39 --output-embeddings-file output_embed
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
40 ]]></command>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
41
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
42 <inputs>
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
43 <expand macro="input_object_params"/>
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
44 <expand macro="output_object_params"/>
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
45 <expand macro="genes-use-input"/>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
46 <section name="adv" title="Advanced Options">
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
47 <expand macro="dims-use-input"/>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
48 <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/>
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
49 <param label="tSNE method" optional="true" name="tsne_method" argument="--tsne-method" type="select" help="Select the method to use to compute the tSNE. Available methods are: Rtsne, Flt-SNE">
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
50 <option value="Rtsne" selected="true">Rtsne</option>
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
51 <option value="Flt-SNE">Flt-SNE</option>
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
52 </param>
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
53 <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE">
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
54 <option value="2" selected="true">2</option>
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
55 <option value="3">3</option>
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
56 </param>
2
fd0fc93b3c87 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
57 <param label="Perplexity" optional="true" name="perplexity" argument="--perplexity" type="integer" help="An integer above 0."/>
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
58 <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/>
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
59 </section>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
60 </inputs>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
61
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
62 <outputs>
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
63 <expand macro="output_files"/>
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
64 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
65 </outputs>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
66
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
67 <tests>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
68 <test>
5
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
69 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-clusters.rds"/>
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
70 <output name="rds_seurat_file" ftype="rdata" >
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
71 <assert_contents>
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
72 <has_size value="5067150" delta="200000"/>
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
73 </assert_contents>
8d9ceaec2c7f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
74 </output>
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
75 </test>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
76 </tests>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
77 <help><![CDATA[
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
78 .. class:: infomark
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
79
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
80 **What it does**
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
81
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
82 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
83 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
84 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
85 types of single cell data.
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
86
1
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
87 Run t-SNE dimensionality reduction on selected features. Has the option of running
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
88 in a reduced dimensional space (i.e. spectral tSNE, recommended), or
13a27436f8ee planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
89 running based on a set of genes.
0
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
90
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
91 -----
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
92
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
93 **Inputs**
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
94
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
95 * RDS object
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
96
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
97 -----
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
98
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
99 **Outputs**
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
100
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
101 * Seurat RDS object
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
102
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
103 .. _Seurat: https://www.nature.com/articles/nbt.4096
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
104 .. _Satija Lab: https://satijalab.org/seurat/
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
105
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
106 @VERSION_HISTORY@
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
107 ]]></help>
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
108 <expand macro="citations" />
3aea769deab1 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
109 </tool>