Mercurial > repos > ebi-gxa > seurat_run_pca

comparison seurat_run_pca.xml @ 0:df80f3d2f9d4 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 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:15:42 -0400
parents
children c4607a42113e
comparison
equal deleted inserted replaced
-1:000000000000 0:df80f3d2f9d4
1 <tool id="seurat_run_pca" name="Seurat RunPCA" version="2.3.1+galaxy1">
2 <description>run a PCA dimensionality reduction</description>
3 <macros>
4 <import>seurat_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[
9 seurat-run-pca.R
10
11 --input-object-file '$input'
12 #if $pc_genes:
13 --pc-genes '$pc-genes'
14 #end if
15 --output-object-file '$output'
16 --output-embeddings-file output_embed
17 --output-loadings-file output_load
18 --output-stdev-file output_sdev
19 #if $pcs_compute:
20 --pcs-compute '$pcs_compute'
21 #end if
22 #if $use_imputed:
23 '$use_imputed'
24 #end if
25
26 ]]></command>
27
28 <inputs>
29 <param name="input" type="data" format="rdata" label="RDS object" />
30 <param name="pc_genes" type="data" format="tabular, txt" optional="True" label="Genes to scale" help="File of gene names to scale/center. Default is all genes in object." />
31 <param name="pcs_compute" type="integer" optional="True" label="Principal components" help="Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance."/>
32 <param name="use_imputed" type="boolean" truevalue="--use-imputed TRUE" falsevalue="" checked="false" label="Use imputed" help="Run PCA on imputed values."/>
33 </inputs>
34
35 <outputs>
36 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
37 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
38 <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/>
39 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/>
40 </outputs>
41
42 <tests>
43 <test>
44 <param name="input" ftype="rdata" value="out_scale.rds"/>
45 <output name="output" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
46 </test>
47 </tests>
48 <help><![CDATA[
49 .. class:: infomark
50
51 **What it does**
52
53 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
54 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
55 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
56 types of single cell data.
57
58 This tool runs a PCA dimensionality reduction
59
60 -----
61
62 **Inputs**
63
64 * Seurat RDS object, normalised and scaled potentially.
65 * Genes used to scale. File of gene names to scale/center. Default is all genes in object.
66 * Principal components to compute. Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance.
67 * Use imputed. Boolean indicating whether to run PCA on imputed values or not.
68
69 -----
70
71 **Outputs**
72
73 * Seurat RDS object with PCA calculations and embeddings.
74 * Embeddings on CSV file. File with a csv-format embeddings table with principal components by cell.
75 * Loadings on CSV file. File with a csv-format loadings table with principal components by gene.
76 * Standard deviation on CSV file. Contains principal components std. deviations.
77
78 .. _Seurat: https://www.nature.com/articles/nbt.4096
79 .. _Satija Lab: https://satijalab.org/seurat/
80
81 @VERSION_HISTORY@
82 ]]></help>
83 <expand macro="citations" />
84 </tool>