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comparison seurat.xml @ 1:7319f83ae734 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 88cf23c767023f71b4ea1e72aac568cc694cc34a"
author iuc
date Mon, 09 Dec 2019 14:32:16 -0500
parents 8d8412d35247
children 321bdd834266
comparison
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0:8d8412d35247 1:7319f83ae734
1 <tool id="seurat" name="Seurat" version="2.3.4"> 1 <tool id="seurat" name="Seurat" version="2.3.4">
2 <description>- toolkit for exploration of single-cell RNA-seq data</description> 2 <description>- toolkit for exploration of single-cell RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement> 4 <requirement type="package" version="3.1.0">r-seurat</requirement>
5 <requirement type="package" version="2.3.4">r-seurat</requirement> 5 <requirement type="package" version="1.16">r-rmarkdown</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> 6 </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[ 7 <command detect_errors="exit_code"><![CDATA[
13 8 #if "vln" in $meta.plots:
14 #if $rscript: 9 #set $vln = 'T'
15 cp '$__tool_directory__/seurat.R' '$out_rscript' && 10 #else
11 #set $vln = 'F'
16 #end if 12 #end if
17 13 #if "feat" in $meta.plots:
18 Rscript '$__tool_directory__/seurat.R' 14 #set $feat = 'T'
19 15 #else
20 --counts '$counts' 16 #set $feat = 'F'
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 17 #end if
28 #if $adv.high_thresholds: 18 #if "PCs" in $meta.plots:
29 --high.thresholds $adv.high_thresholds 19 #set $PCs = 'T'
20 #else
21 #set $PCs = 'F'
30 #end if 22 #end if
31 #if $adv.x_low_cutoff: 23 #if "tsne" in $meta.plots:
32 --x.low.cutoff $adv.x_low_cutoff 24 #set $tsne = 'T'
25 #else
26 #set $tsne = 'F'
33 #end if 27 #end if
34 #if $adv.x_high_cutoff: 28 #if "heat" in $meta.plots:
35 --x.high.cutoff $adv.x_high_cutoff 29 #set $heatmaps = 'T'
30 #else
31 #set $heatmaps = 'F'
36 #end if 32 #end if
37 #if $adv.y_cutoff: 33 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
38 --y.cutoff $adv.y_cutoff 34 params = list(counts = \"${counts}\",
39 #end if 35 min_cells = \"${adv.min_cells}\",
40 #if $adv.cells_use: 36 min_genes = \"${adv.min_genes}\",
41 --cells.use $adv.cells_use 37 low_thresholds = \"${adv.low_thresholds}\",
42 #end if 38 high_thresholds = \"${adv.high_thresholds}\",
43 #if $adv.resolution: 39 numPCs = \"${adv.num_PCs}\",
44 --resolution $adv.resolution 40 cells_use = \"${adv.cells_use}\",
45 #end if 41 resolution = \"${adv.resolution}\",
46 #if $adv.min_pct: 42 min_pct = \"${adv.min_pct}\",
47 --min.pct $adv.min_pct 43 logfc_threshold = \"${adv.logfc_threshold}\",
48 #end if 44 warn = \"${meta.warn}\",
49 #if $adv.logfc_threshold: 45 varstate = \"${meta.varstate}\",
50 --logfc.threshold $adv.logfc_threshold 46 showcode = \"${meta.showcode}\",
51 #end if 47 vlnfeat = \"$vln\",
52 48 featplot = \"$feat\",
53 #if $rds: 49 PCplots = \"$PCs\",
54 --rds '$rds' 50 tsne = \"$tsne\",
55 #end if 51 heatmaps = \"$heatmaps\"),
56 52 intermediates_dir = \".\",
57 ]]></command> 53 output_format = html_document(),
58 54 output_dir = \".\",
55 output_file = \"out.html\")"
56 ]]></command>
59 <inputs> 57 <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"/> 58 <param name="counts" type="data" format="tabular,tsv" 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" /> 59 <section name="adv" title="Advanced Options" expanded="true">
62 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Seurat RDS object?" 60 <param name="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" />
63 help="Output the Seurat RDS object, can be loaded into R. Default: No"> 61 <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells." />
64 </param> 62 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." />
65 <section name="adv" title="Advanced Options"> 63 <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" />
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" /> 64 <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" />
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." /> 65 <param name="cells_use" type="integer" min="1" value="500" 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" />
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." /> 66 <param name="resolution" type="float" value="0.6" 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." />
69 <param argument="--low_thresholds" type="float" optional="True" label="Low threshold for filtering cells" /> 67 <param name="min_pct" type="float" value="0.1" 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" />
70 <param argument="--high_thresholds" type="float" optional="True" label="High threshold for filtering cells" /> 68 <param name="logfc_threshold" type="float" min="0" value="0.25" label="LogFC threshold"
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." /> 69 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> 70 </section>
71 <section name="meta" title="Output options" expanded="true">
72 <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/>
73 <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/>
74 <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/>
75 <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?">
76 <option value="vln" selected="true">Violin and Scatter plots</option>
77 <option value="feat" selected="true">Feature counts plots</option>
78 <option value="PCs" selected="true">PC plots</option>
79 <option value="tsne" selected="true">tSNE plots</option>
80 <option value="heat" selected="true">Heatmap plots</option>
81 </param>
82 </section>
80 </inputs> 83 </inputs>
81
82 <outputs> 84 <outputs>
83 <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" /> 85 <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" />
84 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${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> 86 </outputs>
91 87
92 <tests> 88 <tests>
93 <!-- Ensure count matrix input works -->
94 <test> 89 <test>
95 <param name="counts" ftype="tabular" value="deng_small.tab.gz"/> 90 <param name="counts" ftype="tabular" value="counts.tab.gz"/>
96 <param name="min_cells" value="3"/> 91 <section name="adv">
97 <param name="min_genes" value="200"/> 92 <param name="numPCs" value="10" />
98 <param name="low_thresholds" value="1" /> 93 <param name="min_cells" value="3"/>
99 <param name="high_thresholds" value="20000000" /> 94 <param name="min_genes" value="200"/>
100 <param name="x_low_cutoff" value="0.0125" /> 95 <param name="low_thresholds" value="1" />
101 <param name="x_high_cutoff" value="3" /> 96 <param name="high_thresholds" value="20000000" />
102 <param name="y_cutoff" value="0.5" /> 97 <param name="cells_use" value="500"/>
103 <param name="numPCs" value="10" /> 98 <param name="resolution" value="0.6" />
104 <param name="cells_use" value="500"/> 99 <param name="min_pct" value="0.25" />
105 <param name="resolution" value="0.6" /> 100 <param name="logfc_threshold" value="0.25" />
106 <param name="min_pct" value="0.25" /> 101 </section>
107 <param name="logfc_threshold" value="0.25" /> 102 <section name="meta">
108 <output name="out_pdf" ftype="pdf" value="out.pdf" compare="sim_size"/> 103 <param name="showcode" value="T"/>
104 <param name="warn" value="F"/>
105 <param name="varstate" value="F"/>
106 <param name="plots" value="feat"/>
107 </section>
108 <output name="out_html" ftype="html" value="out.html" compare="sim_size"/>
109 </test> 109 </test>
110 </tests> 110 </tests>
111 <help><![CDATA[ 111 <help><![CDATA[
112 .. class:: infomark 112 .. class:: infomark
113 113
126 126
127 ----- 127 -----
128 128
129 **Outputs** 129 **Outputs**
130 130
131 * PDF of plots 131 * HTML of plots
132 132
133 Optionally you can choose to output 133 Optionally you can choose to output
134 134
135 * Seurat RDS object (can use within R) 135 * Seurat RDS object (can use within R)
136 * Rscript 136 * Rscript