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comparison seurat.xml @ 6:764f076e9d52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit e8eeff2efea68e1e5bc697d0ff6a5808cd978db2"
author iuc
date Thu, 23 Jul 2020 11:22:05 -0400
parents 06ed31cf52ed
children 4c139a9415d7
comparison
equal deleted inserted replaced
5:06ed31cf52ed 6:764f076e9d52
1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy2">
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 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.1.5</token> 4 <token name="@TOOL_VERSION@">3.1.5</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
40 #if "heat" in $meta.plots: 40 #if "heat" in $meta.plots:
41 #set $heatmaps = 'T' 41 #set $heatmaps = 'T'
42 #else 42 #else
43 #set $heatmaps = 'F' 43 #set $heatmaps = 'F'
44 #end if 44 #end if
45 #if not str($adv.perplexity):
46 #set $adv_perplexity = -1
47 #else:
48 #set $adv_perplexity = $adv.perplexity
49 #end if
45 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", 50 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
46 params = list(counts = \"${counts}\", 51 params = list(counts = \"${counts}\",
47 min_cells = \"${adv.min_cells}\", 52 min_cells = \"${adv.min_cells}\",
48 min_genes = \"${adv.min_genes}\", 53 min_genes = \"${adv.min_genes}\",
49 low_thresholds = \"${adv.low_thresholds}\", 54 low_thresholds = \"${adv.low_thresholds}\",
50 high_thresholds = \"${adv.high_thresholds}\", 55 high_thresholds = \"${adv.high_thresholds}\",
51 numPCs = \"${adv.num_PCs}\", 56 numPCs = \"${adv.num_PCs}\",
52 cells_use = \"${adv.cells_use}\", 57 cells_use = \"${adv.cells_use}\",
53 resolution = \"${adv.resolution}\", 58 resolution = \"${adv.resolution}\",
59 perplexity = \"${adv_perplexity}\",
54 min_pct = \"${adv.min_pct}\", 60 min_pct = \"${adv.min_pct}\",
55 logfc_threshold = \"${adv.logfc_threshold}\", 61 logfc_threshold = \"${adv.logfc_threshold}\",
56 warn = \"${meta.warn}\", 62 warn = \"${meta.warn}\",
57 varstate = \"${meta.varstate}\", 63 varstate = \"${meta.varstate}\",
58 showcode = \"${meta.showcode}\", 64 showcode = \"${meta.showcode}\",
74 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." /> 80 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." />
75 <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" /> 81 <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" />
76 <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" /> 82 <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" />
77 <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" /> 83 <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" />
78 <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." /> 84 <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." />
85 <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" />
79 <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" /> 86 <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" />
80 <param name="logfc_threshold" type="float" min="0" value="0.25" label="LogFC threshold" 87 <param name="logfc_threshold" type="float" min="0" value="0.25" label="LogFC threshold"
81 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." /> 88 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." />
82 </section> 89 </section>
83 <section name="meta" title="Output options" expanded="true"> 90 <section name="meta" title="Output options" expanded="true">
106 <param name="min_genes" value="200"/> 113 <param name="min_genes" value="200"/>
107 <param name="low_thresholds" value="1" /> 114 <param name="low_thresholds" value="1" />
108 <param name="high_thresholds" value="20000000" /> 115 <param name="high_thresholds" value="20000000" />
109 <param name="cells_use" value="500"/> 116 <param name="cells_use" value="500"/>
110 <param name="resolution" value="0.6" /> 117 <param name="resolution" value="0.6" />
118 <param name="min_pct" value="0.25" />
119 <param name="logfc_threshold" value="0.25" />
120 </section>
121 <section name="meta">
122 <param name="showcode" value="T"/>
123 <param name="warn" value="F"/>
124 <param name="varstate" value="F"/>
125 <param name="plots" value="feat"/>
126 </section>
127 <output name="out_html" ftype="html" value="out.html" compare="sim_size" delta="20000" />
128 </test>
129 <test> <!-- perplexity test -->
130 <param name="counts" ftype="tabular" value="counts.tab.gz"/>
131 <section name="adv">
132 <param name="numPCs" value="10" />
133 <param name="min_cells" value="3"/>
134 <param name="min_genes" value="200"/>
135 <param name="low_thresholds" value="1" />
136 <param name="high_thresholds" value="20000000" />
137 <param name="cells_use" value="500"/>
138 <param name="resolution" value="0.6" />
139 <param name="perplexity" value="16" />
111 <param name="min_pct" value="0.25" /> 140 <param name="min_pct" value="0.25" />
112 <param name="logfc_threshold" value="0.25" /> 141 <param name="logfc_threshold" value="0.25" />
113 </section> 142 </section>
114 <section name="meta"> 143 <section name="meta">
115 <param name="showcode" value="T"/> 144 <param name="showcode" value="T"/>