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annotate seurat.xml @ 7:4c139a9415d7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 8f89414ecee8120447febc2902ff1ddbbd71e638"
author iuc
date Thu, 01 Oct 2020 22:52:35 +0000
parents 764f076e9d52
children 828324f3292f
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4c139a9415d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 8f89414ecee8120447febc2902ff1ddbbd71e638"
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1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0">
0
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2 <description>- toolkit for exploration of single-cell RNA-seq data</description>
2
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.2.2</token>
2
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5 </macros>
0
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
7
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8 <requirement type="package" version="2.4">r-rmarkdown</requirement>
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9 </requirements>
8d8412d35247 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit 24c0223b9baa6d59bba381ef94f7e77b1c204d80
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if "vln" in $meta.plots:
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12 #set $vln = 'T'
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13 #else
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14 #set $vln = 'F'
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15 #end if
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16 #if "feat" in $meta.plots:
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17 #set $feat = 'T'
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18 #else
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19 #set $feat = 'F'
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20 #end if
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21 #if "PCs" in $meta.plots:
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22 #set $PCs = 'T'
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23 #else
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24 #set $PCs = 'F'
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25 #end if
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26 #if "tsne" in $meta.plots:
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27 #set $tsne = 'T'
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28 #else
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29 #set $tsne = 'F'
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30 #end if
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31 #if "heat" in $meta.plots:
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32 #set $heatmaps = 'T'
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33 #else
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34 #set $heatmaps = 'F'
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35 #end if
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36 #if not str($adv.perplexity):
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37 #set $adv_perplexity = -1
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38 #else:
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39 #set $adv_perplexity = $adv.perplexity
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40 #end if
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41 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
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42 params = list(counts = \"${counts}\",
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43 min_cells = \"${adv.min_cells}\",
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44 min_genes = \"${adv.min_genes}\",
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45 low_thresholds = \"${adv.low_thresholds}\",
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46 high_thresholds = \"${adv.high_thresholds}\",
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47 numPCs = \"${adv.num_PCs}\",
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48 cells_use = \"${adv.cells_use}\",
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49 resolution = \"${adv.resolution}\",
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50 perplexity = \"${adv_perplexity}\",
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51 min_pct = \"${adv.min_pct}\",
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52 logfc_threshold = \"${adv.logfc_threshold}\",
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53 warn = \"${meta.warn}\",
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54 varstate = \"${meta.varstate}\",
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55 showcode = \"${meta.showcode}\",
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56 vlnfeat = \"$vln\",
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57 featplot = \"$feat\",
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58 PCplots = \"$PCs\",
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59 tsne = \"$tsne\",
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60 heatmaps = \"$heatmaps\"),
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61 intermediates_dir = \".\",
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62 output_format = html_document(),
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63 output_dir = \".\",
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64 output_file = \"out.html\")"
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65 ]]></command>
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66 <inputs>
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67 <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"/>
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68 <section name="adv" title="Advanced Options" expanded="true">
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69 <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" />
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70 <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." />
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71 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected." />
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72 <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" />
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73 <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" />
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74 <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" />
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75 <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." />
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76 <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" />
1
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77 <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" />
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78 <param name="logfc_threshold" type="float" min="0" value="0.25" label="LogFC threshold"
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79 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." />
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80 </section>
1
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81 <section name="meta" title="Output options" expanded="true">
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82 <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/>
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83 <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/>
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84 <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/>
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85 <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?">
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86 <option value="vln" selected="true">Violin and Scatter plots</option>
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87 <option value="feat" selected="true">Feature counts plots</option>
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88 <option value="PCs" selected="true">PC plots</option>
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89 <option value="tsne" selected="true">tSNE plots</option>
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90 <option value="heat" selected="true">Heatmap plots</option>
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91 </param>
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92 </section>
0
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93 </inputs>
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94 <outputs>
1
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95 <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" />
0
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96 </outputs>
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97
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98 <tests>
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99 <test>
1
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100 <param name="counts" ftype="tabular" value="counts.tab.gz"/>
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101 <section name="adv">
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102 <param name="numPCs" value="10" />
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103 <param name="min_cells" value="3"/>
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104 <param name="min_genes" value="200"/>
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105 <param name="low_thresholds" value="1" />
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106 <param name="high_thresholds" value="20000000" />
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107 <param name="cells_use" value="500"/>
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108 <param name="resolution" value="0.6" />
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109 <param name="min_pct" value="0.25" />
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110 <param name="logfc_threshold" value="0.25" />
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111 </section>
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112 <section name="meta">
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113 <param name="showcode" value="T"/>
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114 <param name="warn" value="F"/>
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115 <param name="varstate" value="F"/>
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116 <param name="plots" value="feat"/>
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117 </section>
3
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118 <output name="out_html" ftype="html" value="out.html" compare="sim_size" delta="20000" />
0
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119 </test>
6
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120 <test> <!-- perplexity test -->
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121 <param name="counts" ftype="tabular" value="counts.tab.gz"/>
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122 <section name="adv">
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123 <param name="numPCs" value="10" />
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124 <param name="min_cells" value="3"/>
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125 <param name="min_genes" value="200"/>
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126 <param name="low_thresholds" value="1" />
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127 <param name="high_thresholds" value="20000000" />
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128 <param name="cells_use" value="500"/>
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129 <param name="resolution" value="0.6" />
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130 <param name="perplexity" value="16" />
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131 <param name="min_pct" value="0.25" />
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132 <param name="logfc_threshold" value="0.25" />
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133 </section>
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134 <section name="meta">
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135 <param name="showcode" value="T"/>
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136 <param name="warn" value="F"/>
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137 <param name="varstate" value="F"/>
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138 <param name="plots" value="feat"/>
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139 </section>
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140 <output name="out_html" ftype="html" value="out.html" compare="sim_size" delta="20000" />
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141 </test>
0
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142 </tests>
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143 <help><![CDATA[
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144 .. class:: infomark
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145
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146 **What it does**
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147
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148 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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149 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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150 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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151 types of single cell data. See the `Seurat Guided Clustering tutorial`_ for more information.
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152
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153 -----
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154
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155 **Inputs**
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156
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157 * Gene count matrix in TAB-separated format
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158
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159 -----
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160
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161 **Outputs**
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162
1
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163 * HTML of plots
0
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164
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165 Optionally you can choose to output
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166
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167 * Seurat RDS object (can use within R)
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168 * Rscript
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169
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170 .. _Seurat: https://www.nature.com/articles/nbt.4096
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171 .. _Satija Lab: https://satijalab.org/seurat/
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172 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html
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173
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174 ]]></help>
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175 <citations>
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176 <citation type="doi">10.1038/nbt.4096</citation>
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177 </citations>
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178 </tool>