Mercurial > repos > ebi-gxa > seurat_run_tsne
comparison seurat_run_tsne.xml @ 0:3aea769deab1 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 11:19:13 -0400 |
parents | |
children | 13a27436f8ee |
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1 <tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1"> | |
2 <description>run t-SNE 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-tsne.R | |
10 | |
11 --input-object-file '$input' | |
12 | |
13 #if $genes_use: | |
14 --genes-use '$genes_use' | |
15 #end if | |
16 | |
17 #if str($adv.dims_use): | |
18 --dims-use \$(seq -s , 1 '$adv.dims_use') | |
19 #else | |
20 --dims-use 1,10 | |
21 #end if | |
22 | |
23 #if not $adv.do_fast: | |
24 --do-fast '$adv.do_fast' | |
25 #end if | |
26 | |
27 --output-object-file '$output' | |
28 --output-embeddings-file output_embed | |
29 ]]></command> | |
30 | |
31 <inputs> | |
32 <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/> | |
33 <expand macro="genes-use-input"/> | |
34 <section name="adv" title="Advanced Options"> | |
35 <expand macro="dims-use-input"/> | |
36 <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/> | |
37 </section> | |
38 </inputs> | |
39 | |
40 <outputs> | |
41 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> | |
42 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/> | |
43 </outputs> | |
44 | |
45 <tests> | |
46 <test> | |
47 <param name="input" ftype="rdata" value="out_findclust.rds"/> | |
48 <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/> | |
49 </test> | |
50 </tests> | |
51 <help><![CDATA[ | |
52 .. class:: infomark | |
53 | |
54 **What it does** | |
55 | |
56 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | |
57 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and | |
58 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse | |
59 types of single cell data. | |
60 | |
61 Run t-SNE dimensionality reduction on selected features. Has the option of | |
62 running in a reduced dimensional space (i.e. spectral tSNE, recommended), | |
63 or running based on a set of genes. For details about stored TSNE calculation | |
64 parameters, see standard output of the tool. | |
65 | |
66 ----- | |
67 | |
68 **Inputs** | |
69 | |
70 * RDS object | |
71 | |
72 ----- | |
73 | |
74 **Outputs** | |
75 | |
76 * Seurat RDS object | |
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> |