Mercurial > repos > ebi-gxa > seurat_filter_cells
comparison seurat_filter_cells.xml @ 0:c1848daebad1 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 11:16:07 -0400 |
parents | |
children | 30982e805f8c |
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1 <tool id="seurat_filter_cells" name="Seurat FilterCells" version="2.3.1+galaxy1"> | |
2 <description>filter cells in a Seurat object</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-filter-cells.R | |
10 | |
11 --input-object-file '$input' | |
12 #if $subset: | |
13 --subset-names '$subset' | |
14 #else | |
15 --subset-names nUMI | |
16 #end if | |
17 #if $low: | |
18 --low-thresholds $low | |
19 #end if | |
20 #if $high: | |
21 --high-thresholds $high | |
22 #end if | |
23 #if $cells: | |
24 --cells-use $cells | |
25 #end if | |
26 --output-object-file '$output' | |
27 ]]></command> | |
28 | |
29 <inputs> | |
30 <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Output from Seurat create object." /> | |
31 <param name="subset" argument="--subset-names" type="text" label="Subset names" optional="True" help="Parameters to subset on. Eg, the name of a gene, PC1, a column name in object@meta.data, etc. Any argument that can be retreived using FetchData. Multiple values can be separated by colons (:)."> | |
32 <validator type="regex" message="Please only use letters or numbers">^[\(\w\)]+$</validator> | |
33 </param> | |
34 <param name="low" argument="--low-thresholds" type="float" optional="True" label="Low threshold for filtering cells" help="Multiple values can be separated by colons (:) and should have same length as provided for `Subset names`." /> | |
35 <param name="high" argument="--high-thresholds" type="float" optional="True" label="High threshold for filtering cells" help="Multiple values can be separated by colons (:) and should have same length as provided for `Subset names`." /> | |
36 <param name="cells" argument="--cells-use" type="text" min="0" optional="True" help="Comma-separated list of cell names to use as a subset." label="Cells to use" /> | |
37 </inputs> | |
38 | |
39 <outputs> | |
40 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> | |
41 </outputs> | |
42 | |
43 <tests> | |
44 <test> | |
45 <param name="input" ftype="rdata" value="seurat.rds"/> | |
46 <output name="output" ftype="rdata" value="out_filter.rds" compare="sim_size"/> | |
47 </test> | |
48 </tests> | |
49 <help><![CDATA[ | |
50 .. class:: infomark | |
51 | |
52 **What it does** | |
53 | |
54 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | |
55 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and | |
56 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse | |
57 types of single cell data. | |
58 | |
59 This tool filters a Seurat RDS object. | |
60 | |
61 ----- | |
62 | |
63 **Inputs** | |
64 | |
65 * Seurat RDS object. Probably the one produced by Seurat create object. | |
66 * Subset names. A list of attributes to subset on, colon separated (:). | |
67 * Low thresholds. A minimum value for each of the attributes set in subset names, again, colon separated (:). Optional. | |
68 * High thresholds. A maximum value for each of the attributes set in subset names, again, colon separated (:). Optional. | |
69 * Cells to use. A list of cell names/idenfifiers to filter positively by. | |
70 | |
71 ----- | |
72 | |
73 **Outputs** | |
74 | |
75 * Seurat RDS object filtered according to the inputs. | |
76 | |
77 .. _Seurat: https://www.nature.com/articles/nbt.4096 | |
78 .. _Satija Lab: https://satijalab.org/seurat/ | |
79 | |
80 @VERSION_HISTORY@ | |
81 | |
82 ]]></help> | |
83 <expand macro="citations" /> | |
84 </tool> |