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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author ebi-gxa
date Mon, 25 Nov 2019 06:09:57 -0500
parents fde95fe95f15
children 4039a99ae846
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0:fde95fe95f15 1:7895b4bb6247
1 <tool id="seurat_find_markers" name="Seurat FindMarkers" version="2.3.1+galaxy1"> 1 <tool id="seurat_find_markers" name="Seurat FindMarkers" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
2 <description>find markers (differentially expressed genes)</description> 2 <description>find markers (differentially expressed genes)</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-find-markers.R 9 seurat-find-markers.R
10 10
11 --input-object-file '$input' 11 @INPUT_OBJECT@
12 --output-text-file output.txt 12 --output-text-file output.txt
13 13
14 #if $genes_use: 14 #if $genes_use:
15 --genes-use '$genes_use' 15 --genes-use '$genes_use'
16 #end if 16 #end if
47 47
48 48
49 ]]></command> 49 ]]></command>
50 50
51 <inputs> 51 <inputs>
52 <param name="input" type="data" format="rdata" label="RDS object" /> 52 <expand macro="input_object_params"/>
53 <expand macro="genes-use-input"/> 53 <expand macro="genes-use-input"/>
54 <param name="logfc_threshold" label="LogFC logfc_threshold" optional="true" argument="--logfc-threshold" type="float" help="Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals."/> 54 <param name="logfc_threshold" label="LogFC logfc_threshold" optional="true" argument="--logfc-threshold" type="float" help="Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals."/>
55 <param name="max_cells_per_ident" label="Max cells per ident" optional="true" argument="--max-cells-per-ident" type="integer" help="Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)."/> 55 <param name="max_cells_per_ident" label="Max cells per ident" optional="true" argument="--max-cells-per-ident" type="integer" help="Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)."/>
56 <param name="min_cells_per_gene" label="Min cells per gene" optional="true" argument="--min-cells-gene" type="integer" help="Minimum number of cells expressing the gene in at least one of the two groups, currently only used for poisson and negative binomial tests."/> 56 <param name="min_cells_per_gene" label="Min cells per gene" optional="true" argument="--min-cells-gene" type="integer" help="Minimum number of cells expressing the gene in at least one of the two groups, currently only used for poisson and negative binomial tests."/>
57 <param name="min_cells_group" label="Min cells in one of the groups" optional="true" argument="--min-cells-group" type="integer"/> 57 <param name="min_cells_group" label="Min cells in one of the groups" optional="true" argument="--min-cells-group" type="integer"/>
72 </param> 72 </param>
73 </section> 73 </section>
74 </inputs> 74 </inputs>
75 75
76 <outputs> 76 <outputs>
77 <data name="output" format="txt" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Text file"/> 77 <data name="output" format="csv" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Text file"/>
78 </outputs> 78 </outputs>
79 79
80 <tests> 80 <tests>
81 <test> 81 <test>
82 <param name="input" ftype="rdata" value="out_runtsne.rds"/> 82 <param name="input" ftype="rdata" value="out_runtsne.rds"/>
86 <help><![CDATA[ 86 <help><![CDATA[
87 .. class:: infomark 87 .. class:: infomark
88 88
89 **What it does** 89 **What it does**
90 90
91 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 91 This tool finds markers (differentially expressed genes) for each of the identity classes in a dataset.
92 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and 92 It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
93 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
94 types of single cell data.
95 93
96 This tool finds markers (differentially expressed genes) for each of the identity classes in a dataset. It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.) 94 p-value adjustment is performed using bonferroni correction based on the total
95 number of genes in the dataset. Other correction methods are not recommended,
96 as Seurat pre-filters genes using the arguments above, reducing the number of
97 tests performed. Lastly, as Aaron Lun has pointed out, p-values should be
98 interpreted cautiously, as the genes used for clustering are the same genes
99 tested for differential expression.
100
101 @SEURAT_INTRO@
97 102
98 ----- 103 -----
99 104
100 **Inputs** 105 **Inputs**
101 106