Mercurial > repos > ebi-gxa > seurat_read10x
comparison seurat_read10x.xml @ 0:1b8566f3c1d0 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 11:18:21 -0400 |
parents | |
children | 265dcc5bc1e8 |
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1 <tool id="seurat_read10x" name="Seurat Read10x" version="2.3.1+galaxy1"> | |
2 <description>Loads 10x data into a serialized seurat R object</description> | |
3 <macros> | |
4 <import>seurat_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <stdio> | |
8 <exit_code range="1:" /> | |
9 </stdio> | |
10 <command><![CDATA[ | |
11 ln -s "$matrix" matrix.mtx; | |
12 ln -s "$genes" genes.tsv; | |
13 ln -s "$barcodes" barcodes.tsv; | |
14 | |
15 seurat-read-10x.R -d ./ -o "$R_seurat_serialized" | |
16 ]]></command> | |
17 <inputs> | |
18 <param type="data" name="matrix" help="Raw expression quantification as a sparse matrix in Matrix Market format, where each column is a gene and each row is a barcode/cell." format="txt" label="Expression matrix in sparse matrix format (.mtx)" /> | |
19 <param type="data" name="genes" help="Matrix market column file for genes" label="Gene table" format="tsv,tabular"/> | |
20 <param type="data" name="barcodes" help="Matrix market row file for genes" label="Barcode/cell table" format="tsv,tabular"/> | |
21 </inputs> | |
22 <outputs> | |
23 <data name="R_seurat_serialized" format="rdata" label="${tool.name} on ${on_string}: RData file" /> | |
24 </outputs> | |
25 | |
26 <tests> | |
27 <test> | |
28 <param name="matrix" ftype="txt" value="test_matrix.txt"/> | |
29 <param name="genes" ftype="txt" value="test_genes.txt"/> | |
30 <param name="barcodes" ftype="txt" value="test_barcodes.txt"/> | |
31 <output name="R_seurat_serialized" ftype="rdata" value="out_scale.rds" compare="sim_size"/> | |
32 </test> | |
33 </tests> | |
34 | |
35 | |
36 <help><![CDATA[ | |
37 .. class:: infomark | |
38 | |
39 **What it does** | |
40 | |
41 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | |
42 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and | |
43 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse | |
44 types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information. | |
45 | |
46 **Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)** | |
47 | |
48 The mtx directory should contain: | |
49 | |
50 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. | |
51 | |
52 2) A gene table of at least two columns where the first column gives the gene IDs. | |
53 | |
54 3) A barcode/cell table of at least one column giving the barcode/cell IDs. | |
55 | |
56 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` | |
57 with a dataset accession. Otherwise, they need to be provided as separate Galaxy | |
58 datasets. | |
59 | |
60 **Inputs** | |
61 * Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. | |
62 * A gene table of at least two columns where the first column gives the gene IDs. | |
63 * A barcode/cell table of at least one column giving the barcode/cell IDs. | |
64 | |
65 **Outputs** | |
66 * R object for Seurat | |
67 | |
68 .. _Seurat: https://www.nature.com/articles/nbt.4096 | |
69 .. _Satija Lab: https://satijalab.org/seurat/ | |
70 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html | |
71 | |
72 @VERSION_HISTORY@ | |
73 ]]></help> | |
74 <expand macro="citations"/> | |
75 </tool> |