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comparison seurat.xml @ 0:8d8412d35247 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
author iuc
date Sun, 26 Aug 2018 16:24:02 -0400
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children 7319f83ae734
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-1:000000000000 0:8d8412d35247
1 <tool id="seurat" name="Seurat" version="2.3.4">
2 <description>- toolkit for exploration of single-cell RNA-seq data</description>
3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="2.3.4">r-seurat</requirement>
6 <requirement type="package" version="1.0.0">bioconductor-singlecellexperiment</requirement>
7 <requirement type="package" version="1.6.0">r-optparse</requirement>
8 </requirements>
9 <version_command><![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", SingleCellExperiment version" $(R --vanilla --slave -e "library(SingleCellExperiment); cat(sessionInfo()\$otherPkgs\$SingleCellExperiment\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
11 ]]></version_command>
12 <command detect_errors="exit_code"><![CDATA[
13
14 #if $rscript:
15 cp '$__tool_directory__/seurat.R' '$out_rscript' &&
16 #end if
17
18 Rscript '$__tool_directory__/seurat.R'
19
20 --counts '$counts'
21 --numPCs $adv.num_PCs
22 --min.cells $adv.min_cells
23 --min.genes $adv.min_genes
24
25 #if $adv.low_thresholds:
26 --low.thresholds $adv.low_thresholds
27 #end if
28 #if $adv.high_thresholds:
29 --high.thresholds $adv.high_thresholds
30 #end if
31 #if $adv.x_low_cutoff:
32 --x.low.cutoff $adv.x_low_cutoff
33 #end if
34 #if $adv.x_high_cutoff:
35 --x.high.cutoff $adv.x_high_cutoff
36 #end if
37 #if $adv.y_cutoff:
38 --y.cutoff $adv.y_cutoff
39 #end if
40 #if $adv.cells_use:
41 --cells.use $adv.cells_use
42 #end if
43 #if $adv.resolution:
44 --resolution $adv.resolution
45 #end if
46 #if $adv.min_pct:
47 --min.pct $adv.min_pct
48 #end if
49 #if $adv.logfc_threshold:
50 --logfc.threshold $adv.logfc_threshold
51 #end if
52
53 #if $rds:
54 --rds '$rds'
55 #end if
56
57 ]]></command>
58
59 <inputs>
60 <param name="counts" type="data" format="tabular" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
61 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used by this tool will be provided as a text file in the output. Default: No" />
62 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Seurat RDS object?"
63 help="Output the Seurat RDS object, can be loaded into R. Default: No">
64 </param>
65 <section name="adv" title="Advanced Options">
66 <param argument="--num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE. Default: 10" />
67 <param argument="--min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells." />
68 <param argument="--min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." />
69 <param argument="--low_thresholds" type="float" optional="True" label="Low threshold for filtering cells" />
70 <param argument="--high_thresholds" type="float" optional="True" label="High threshold for filtering cells" />
71 <param argument="--x_low_cutoff" type="float" optional="True" label="X-axis low cutoff for variable genes" help="Bottom cutoff on x-axis for identifying variable genes" />
72 <param argument="--x_high_cutoff" type="float" optional="True" label="X-axis high cutoff for variable genes" help="Top cutoff on x-axis for identifying variable genes" />
73 <param argument="--y_cutoff" type="float" optional="True" label="Y-axis cutoff for variable genes" help="Bottom cutoff on y-axis for identifying variable genes" />
74 <param argument="--cells_use" type="integer" min="0" optional="True" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" />
75 <param argument="--resolution" type="float" optional="True" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities." />
76 <param argument="--min_pct" type="float" optional="True" label="Minimum percent cells" help="With FindMarkers only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1" />
77 <param argument="--logfc_threshold" type="float" min="0" optional="True" label="LogFC threshold"
78 help="With FindMarkers, 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." />
79 </section>
80 </inputs>
81
82 <outputs>
83 <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" />
84 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
85 <filter>rscript</filter>
86 </data>
87 <data name="out_rds" format="rds" from_work_dir="Seurat.rds" label="${tool.name} on ${on_string}: RData file">
88 <filter>rds</filter>
89 </data>
90 </outputs>
91
92 <tests>
93 <!-- Ensure count matrix input works -->
94 <test>
95 <param name="counts" ftype="tabular" value="deng_small.tab.gz"/>
96 <param name="min_cells" value="3"/>
97 <param name="min_genes" value="200"/>
98 <param name="low_thresholds" value="1" />
99 <param name="high_thresholds" value="20000000" />
100 <param name="x_low_cutoff" value="0.0125" />
101 <param name="x_high_cutoff" value="3" />
102 <param name="y_cutoff" value="0.5" />
103 <param name="numPCs" value="10" />
104 <param name="cells_use" value="500"/>
105 <param name="resolution" value="0.6" />
106 <param name="min_pct" value="0.25" />
107 <param name="logfc_threshold" value="0.25" />
108 <output name="out_pdf" ftype="pdf" value="out.pdf" compare="sim_size"/>
109 </test>
110 </tests>
111 <help><![CDATA[
112 .. class:: infomark
113
114 **What it does**
115
116 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
117 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
118 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
119 types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information.
120
121 -----
122
123 **Inputs**
124
125 * Gene count matrix in TAB-separated format
126
127 -----
128
129 **Outputs**
130
131 * PDF of plots
132
133 Optionally you can choose to output
134
135 * Seurat RDS object (can use within R)
136 * Rscript
137
138 .. _Seurat: https://www.nature.com/articles/nbt.4096
139 .. _Satija Lab: https://satijalab.org/seurat/
140 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html
141
142 ]]></help>
143 <citations>
144 <citation type="doi">10.1038/nbt.4096</citation>
145 </citations>
146 </tool>