Mercurial > repos > ebi-gxa > seurat_export_cellbrowser
comparison seurat_export_cellbrowser.xml @ 0:8c2b1d2659df draft
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 11:16:38 -0400 |
parents | |
children | 80eec773c961 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:8c2b1d2659df |
---|---|
1 <tool id="seurat_export_cellbrowser" name="Seurat Export2CellBrowser" version="2.3.1+galaxy0"> | |
2 <description>produces files for UCSC CellBrowser import.</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 #if $markers_file: | |
10 cp '$markers_file' markers.csv; | |
11 #end if | |
12 | |
13 seurat-export-cellbrowser.R -i '$rds_input' | |
14 | |
15 #if $markers_file: | |
16 -m markers.csv | |
17 #end if | |
18 | |
19 -o output_html; | |
20 | |
21 cd output_html && tar -cf '$output' *; | |
22 ]]></command> | |
23 | |
24 <inputs> | |
25 <param name="rds_input" type="data" format="rdata" label="Seurat RDS object" /> | |
26 <param name="markers_file" type="data" format="txt" label="Marker genes file from Seurat" /> | |
27 </inputs> | |
28 | |
29 <outputs> | |
30 <data name="output" format="tar" label="${tool.name} on ${on_string}: UCSC CellBrowser bundle"/> | |
31 </outputs> | |
32 | |
33 <tests> | |
34 <test> | |
35 <param name="rds_input" ftype="rdata" value="out_runtsne.rds"/> | |
36 <param name="markers_file" ftype="txt" value="out_markers.csv"/> | |
37 <output name="output" ftype="tar" value="out_cellbrowser_bundle.tar"/> | |
38 </test> | |
39 </tests> | |
40 <help><![CDATA[ | |
41 .. class:: infomark | |
42 | |
43 **What it does** | |
44 | |
45 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | |
46 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and | |
47 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse | |
48 types of single cell data. | |
49 | |
50 This tool converts a Seurat object (hopefully with t-SNE results) and its accompanying marker genes file (optional) | |
51 to a tar that can be feed to the UCSC CellBrowser tool. | |
52 ----- | |
53 | |
54 **Inputs** | |
55 | |
56 * RDS object | |
57 | |
58 ----- | |
59 | |
60 **Outputs** | |
61 | |
62 * Text file | |
63 | |
64 .. _Seurat: https://www.nature.com/articles/nbt.4096 | |
65 .. _Satija Lab: https://satijalab.org/seurat/ | |
66 | |
67 @VERSION_HISTORY@ | |
68 | |
69 ]]></help> | |
70 <expand macro="citations" /> | |
71 </tool> |