Mercurial > repos > ebi-gxa > seurat_dim_plot

annotate seurat_macros.xml @ 3:e7e01a7fea38 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f3077a71c898b86794a0d630d11334788b797f2f"
author ebi-gxa
date Sat, 11 Jul 2020 08:44:27 -0400
parents 34f8d81f9d75
children cfc3d8ee3a64
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
1 <?xml version="1.0"?>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
2 <macros>
2
34f8d81f9d75 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
3 <token name="@VERSION@">0.0.7</token>
1
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
4 <token name="@SEURAT_VERSION@">3.1.1</token>
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
5 <xml name="requirements">
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
6 <requirements>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
8 </requirements>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
9 </xml>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
10 <xml name="version">
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
11 <version_command><![CDATA[
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
13 ]]></version_command>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
14 </xml>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
15
1
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
16 <xml name="input_object_params">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
17 <conditional name="input" label="Input format">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
18 <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
20 <option value="loom">Loom</option>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
21 <option value="anndata">AnnData</option>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
22 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
23 </param>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
24 <when value="anndata">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
25 <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
26 </when>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
27 <when value="loom">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
28 <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
29 </when>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
30 <when value="rds_seurat">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
31 <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
32 </when>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
33 <when value="rds_sce">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
34 <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
35 </when>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
36 </conditional>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
37 </xml>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
38
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
39 <token name="@INPUT_OBJECT@">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
40 #if $input.format == "anndata"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
41 --input-object-file '$input.anndata_file' --input-format anndata
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
42 #else if $input.format == "loom"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
43 --input-object-file '$input.loom_file' --input-format loom
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
44 #else if $input.format == "rds_seurat"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
45 --input-object-file '$input.rds_seurat_file' --input-format seurat
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
46 #else if $input.format == "rds_sce"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
47 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
48 #end if
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
49 </token>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
50
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
51 <xml name="output_object_params">
daeca8f7a26e 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 type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
53 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
daeca8f7a26e 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="loom">Loom</option>
daeca8f7a26e 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="rds_sce">RDS with a Single Cell Experiment object</option>
daeca8f7a26e 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>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
57 </xml>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
58
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
59 <xml name="output_files">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
60 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
61 <filter>format == 'loom'</filter>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
62 </data>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
63 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
64 <filter>format == 'rds_seurat'</filter>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
65 </data>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
66 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
67 <filter>format == 'rds_sce'</filter>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
68 </data>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
69 </xml>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
70
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
71 <token name="@OUTPUT_OBJECT@">
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
72 #if $format == "anndata"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
73 --output-object-file '$anndata_file' --output-format anndata
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
74 #else if $format == "loom"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
75 --output-object-file seurat_obj.loom --output-format loom
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
76 #else if $format == "rds_seurat"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
77 --output-object-file '$rds_seurat_file' --output-format seurat
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
78 #else if $format == "rds_sce"
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
79 --output-object-file '$rds_sce_file' --output-format singlecellexperiment
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
80 #end if
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
81 </token>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
82
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
83 <xml name="genes-use-input">
1
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
84 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
85 </xml>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
86 <xml name="dims-use-input">
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
87 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
88 </xml>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
89
1
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
90 <token name="@SEURAT_INTRO@"><![CDATA[
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
91 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
92 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
93 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
94 types of single cell data.
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
95 ]]></token>
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
96
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
97 <token name="@VERSION_HISTORY@"><![CDATA[
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
98 **Version history**
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
99
2
34f8d81f9d75 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
100 3.1.1_0.0.7: Exposes perplexity and enables tab input.
34f8d81f9d75 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
101
1
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
102 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
103
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
104 Find clusters: removed dims-use, k-param, prune-snn.
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
105
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
106 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
107 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l).
1
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
108
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
109 0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9.
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
110 ]]></token>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
111
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
112
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
113 <xml name="citations">
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
114 <citations>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
115 <citation type="doi">10.1038/nbt.4096</citation>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
116 <citation type="bibtex">
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
117 @misc{r-seurat-scripts.git,
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
118 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
119 year = {2018},
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
120 title = {Seurat-scripts: command line interface for Seurat},
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
121 publisher = {GitHub},
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
122 journal = {GitHub repository},
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
123 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
124 }
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
125 </citation>
2
34f8d81f9d75 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
ebi-gxa
parents: 1
diff changeset
126 <citation type="doi">10.1101/2020.04.08.032698</citation>
0
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
127 </citations>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
128 </xml>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
129 </macros>