Mercurial > repos > ebi-gxa > seurat_find_clusters

annotate seurat_find_clusters.xml @ 5:eefaffdcd441 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 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:25:55 +0000
parents 8ed848ef86fd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
eefaffdcd441 "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_find_clusters" name="Seurat FindClusters" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
2 <description>find clusters of cells</description>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
3 <macros>
8ea738667314 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>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
5 </macros>
8ea738667314 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" />
8ea738667314 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" />
8ea738667314 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[
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
9 seurat-find-clusters.R
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
10
1
bdabb6af06e4 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@
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
12 @OUTPUT_OBJECT@
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
13 --output-text-file output_tab
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
14
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
15 #if str($adv.resolution):
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
16 --resolution '$adv.resolution'
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
17 #end if
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
18
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
19 #if str($adv.algorithm):
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
20 --algorithm '$adv.algorithm'
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
21 #end if
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
22
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
23 #if str($adv.modularity_fxn):
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
24 --modularity-fxn '$adv.modularity_fxn'
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
25 #end if
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
26
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
27 #if str($adv.method):
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
28 --method '$adv.method'
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
29 #end if
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
30
bdabb6af06e4 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 str($adv.graph_name):
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
32 --graph-name '$adv.graph_name'
bdabb6af06e4 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
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
34
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
35 #if str($adv.nrandom_starts):
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
36 --nrandom-starts '$adv.nrandom_starts'
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
37 #end if
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
38
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
39 $adv.group_singletons
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
40
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
41
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
42
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
43 ## TODO add pdf support as optional
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
44 ]]></command>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
45
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
46 <inputs>
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
47 <expand macro="input_object_params"/>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
48 <expand macro="output_object_params"/>
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
49 <section name="adv" title="Advanced Options">
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
50 <param name="resolution" argument="--resolution" optional="true" type="float" label="Resolution" help="Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities. Defaults to 0.8."/>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
51 <param name="algorithm" argument="--algorithm" optional="true" type="select" label="Modularity organization algorithm">
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
52 <option value="1" selected="true">Louvain</option>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
53 <option value="2">Louvain algorithm with multilevel refinement</option>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
54 <option value="3">SLM algorithm</option>
1
bdabb6af06e4 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="4">Leiden</option>
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
56 </param>
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
57 <param name="modularity_fxn" argument="--modularity-fxn" optional="true" type="select" label="Modularity function">
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
58 <option value="1" selected="true">Standard</option>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
59 <option value="2">Alternative</option>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
60 </param>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
61 <param name="method" argument="--method" type="select" label="Method for Leiden" help="Method for leiden (defaults to matrix which is fast for small datasets). Select iGraph to avoid casting large data to a dense matrix.">
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
62 <option value="matrix" selected="true">Matrix</option>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
63 <option value="igraph">iGraph</option>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
64 </param>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
65 <param name="graph_name" argument="--graph-name" type="text" value="RNA_nn" label="Graph Name" help="Name of graph to use for the clustering algorith."/>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
66 <param name="nrandom_starts" argument="--nrandom-starts" type="integer" optional="true" label="Random starts" help="Number of random starts, 10 by default."/>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
67 <param name="group_singletons" argument="--group-singletons" type="boolean" truevalue="--group-singletons" falsevalue="" checked="false" label="Group singletons" help="Group singletons into nearest cluster. If FALSE, assign all singletons to a 'singleton' group."/>
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
68 <param name="random_seed" argument="--random-seed" type="integer" optional="true" label="Random seed" help="Seed of the random number generator"/>
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
69 </section>
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
70
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
71 </inputs>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
72 <outputs>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
73 <!-- <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" /> -->
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
74 <expand macro="output_files"/>
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
75 <data name="output_tab" format="csv" from_work_dir="output_tab" label="${tool.name} on ${on_string}: CSV Seurat Clusters"/>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
76 </outputs>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
77
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
78 <tests>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
79 <!-- Ensure count matrix input works -->
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
80 <test>
5
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
81 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-neighbours.rds"/>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
82 <output name="rds_seurat_file" ftype="rdata" >
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
83 <assert_contents>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
84 <has_size value="5064329" delta="200000"/>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
85 </assert_contents>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
86 </output>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
87 <output name="output_tab" >
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
88 <assert_contents>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
89 <has_n_lines n="92" />
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
90 </assert_contents>
eefaffdcd441 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
ebi-gxa
parents: 4
diff changeset
91 </output>
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
92 </test>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
93 </tests>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
94 <help><![CDATA[
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
95 .. class:: infomark
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
96
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
97 **What it does**
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
98
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
99 Identify clusters of cells by a shared nearest neighbor (SNN) modularity optimization
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
100 based clustering algorithm. First calculate k-nearest neighbors and construct t
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
101 he SNN graph (using Seurat find neighbours).
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
102 Then optimize the modularity function to determine clusters.
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
103 For a full description of the algorithms, see Waltman and van Eck (2013)
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
104 The European Physical Journal B.
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
105
1
bdabb6af06e4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
ebi-gxa
parents: 0
diff changeset
106 @SEURAT_INTRO@
0
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
107
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
108 -----
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
109
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
110 **Inputs**
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
111
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
112 * RDS object
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
113
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
114 -----
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
115
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
116 **Outputs**
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
117
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
118 * Seurat RDS object
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
119
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
120 .. _Seurat: https://www.nature.com/articles/nbt.4096
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
121 .. _Satija Lab: https://satijalab.org/seurat/
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
122
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
123 @VERSION_HISTORY@
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
124
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
125 ]]></help>
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
126 <expand macro="citations" />
8ea738667314 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
parents:
diff changeset
127 </tool>