Mercurial > repos > ebi-gxa > seurat_normalise_data
comparison seurat_normalise_data.xml @ 1:48174ec556de draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author | ebi-gxa |
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date | Mon, 25 Nov 2019 06:13:04 -0500 |
parents | 619fead82856 |
children | 9d92ec597603 |
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0:619fead82856 | 1:48174ec556de |
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1 <tool id="seurat_normalise_data" name="Seurat NormaliseData" version="2.3.1+galaxy1"> | 1 <tool id="seurat_normalise_data" name="Seurat NormaliseData" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> |
2 <description>normalise data</description> | 2 <description>normalise data</description> |
3 <macros> | 3 <macros> |
4 <import>seurat_macros.xml</import> | 4 <import>seurat_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="version" /> | 7 <expand macro="version" /> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 seurat-normalise-data.R | 9 seurat-normalise-data.R |
10 | 10 |
11 --input-object-file '$input' | 11 @INPUT_OBJECT@ |
12 #if $norm: | 12 #if $norm: |
13 --normalization-method $norm | 13 --normalization-method $norm |
14 #end if | 14 #end if |
15 #if $assay: | 15 #if $assay: |
16 --assay-type '$assay' | 16 --assay-type '$assay' |
17 #end if | 17 #end if |
18 #if $scale: | 18 #if $scale: |
19 --scale-factor $scale | 19 --scale-factor $scale |
20 #end if | 20 #end if |
21 --output-object-file '$output' | 21 @OUTPUT_OBJECT@ |
22 ]]></command> | 22 ]]></command> |
23 | 23 |
24 <inputs> | 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." /> | 25 <expand macro="input_object_params"/> |
26 <param name="norm" argument="--normalization-method" type="text" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize)."/> | 26 <expand macro="output_object_params"/> |
27 <param name="norm" argument="--normalization-method" type="select" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize). Can be 'CLR' or 'RC' additionally."> | |
28 <option value="LogNormalize" selected="true">Log Normalise</option> | |
29 <option value="CLR">CLR</option> | |
30 <option value="RC">RC</option> | |
31 </param> | |
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."> | 32 <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> | 33 <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator> |
29 </param> | 34 </param> |
30 <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/> | 35 <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/> |
31 </inputs> | 36 </inputs> |
32 | 37 |
33 <outputs> | 38 <outputs> |
34 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/> | 39 <expand macro="output_files"/> |
35 </outputs> | 40 </outputs> |
36 | 41 |
37 <tests> | 42 <tests> |
38 <test> | 43 <test> |
39 <param name="input" ftype="rdata" value="seurat.rds"/> | 44 <param name="input" ftype="rdata" value="seurat.rds"/> |
40 <output name="output" ftype="rdata" value="out_norm.rds" compare="sim_size"/> | 45 <output name="rds_seurat_file" ftype="rdata" value="out_norm.rds" compare="sim_size"/> |
41 </test> | 46 </test> |
42 </tests> | 47 </tests> |
43 <help><![CDATA[ | 48 <help><![CDATA[ |
44 .. class:: infomark | 49 .. class:: infomark |
45 | 50 |
46 **What it does** | 51 **What it does** |
47 | 52 |
48 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | 53 This tool normalises a Seurat RDS object. |
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 | 54 |
53 This tool normalises a Seurat RDS object. | 55 @SEURAT_INTRO@ |
54 | 56 |
55 ----- | 57 ----- |
56 | 58 |
57 **Inputs** | 59 **Inputs** |
58 | 60 |