Mercurial > repos > ebi-gxa > seurat_normalise_data
comparison seurat_normalise_data.xml @ 0:619fead82856 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:20:42 -0400 |
parents | |
children | 48174ec556de |
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1 <tool id="seurat_normalise_data" name="Seurat NormaliseData" version="2.3.1+galaxy1"> | |
2 <description>normalise data</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-normalise-data.R | |
10 | |
11 --input-object-file '$input' | |
12 #if $norm: | |
13 --normalization-method $norm | |
14 #end if | |
15 #if $assay: | |
16 --assay-type '$assay' | |
17 #end if | |
18 #if $scale: | |
19 --scale-factor $scale | |
20 #end if | |
21 --output-object-file '$output' | |
22 ]]></command> | |
23 | |
24 <inputs> | |
25 <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Possibly the output of Seurat filter cells or Seurat create object." /> | |
26 <param name="norm" argument="--normalization-method" type="text" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize)."/> | |
27 <param name="assay" argument="--assay-type" type="text" optional="True" label="Assay type" help = "Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses."> | |
28 <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator> | |
29 </param> | |
30 <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/> | |
31 </inputs> | |
32 | |
33 <outputs> | |
34 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/> | |
35 </outputs> | |
36 | |
37 <tests> | |
38 <test> | |
39 <param name="input" ftype="rdata" value="seurat.rds"/> | |
40 <output name="output" ftype="rdata" value="out_norm.rds" compare="sim_size"/> | |
41 </test> | |
42 </tests> | |
43 <help><![CDATA[ | |
44 .. class:: infomark | |
45 | |
46 **What it does** | |
47 | |
48 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | |
49 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and | |
50 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse | |
51 types of single cell data. | |
52 | |
53 This tool normalises a Seurat RDS object. | |
54 | |
55 ----- | |
56 | |
57 **Inputs** | |
58 | |
59 * Seurat RDS object. Possibly the output of Seurat filter cells or Seurat create object. | |
60 * Normalisation method. Method for normalization. Default is log-normalization (LogNormalize). | |
61 * Assay type. Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses. | |
62 * Scale factor. Sets the scale factor for cell-level normalization. Default: 1000 | |
63 | |
64 ----- | |
65 | |
66 **Outputs** | |
67 | |
68 * Seurat RDS object with normalised matrix. | |
69 | |
70 .. _Seurat: https://www.nature.com/articles/nbt.4096 | |
71 .. _Satija Lab: https://satijalab.org/seurat/ | |
72 | |
73 @VERSION_HISTORY@ | |
74 ]]></help> | |
75 <expand macro="citations" /> | |
76 </tool> |