Mercurial > repos > iuc > raceid_main

annotate raceid_main.xml @ 0:e01c989c7543 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author iuc
date Sat, 03 Mar 2018 17:34:16 -0500
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e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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1 <tool id="raceid_main" name="RaceID" version="@VERSION@.0">
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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2 <description>Race ID pipeline for single-cell RNA analysis</description>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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3 <macros>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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4 <import>macros.xml</import>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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5 </macros>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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6 <expand macro="requirements" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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7
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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8 <command detect_errors="exit_code"><![CDATA[
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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9 ## Filter
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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10 echo "Filtering" &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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11 Rscript '@SCRIPT_DIR@/raceID_filter.R' '@SCRIPT_DIR@' '$rconf_source_filter' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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12
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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13 ## Kmeans
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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14 echo "K-means" &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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15 Rscript '@SCRIPT_DIR@/raceID_kmeans_heatmap.R' '@SCRIPT_DIR@' '$rconf_source_kmeans' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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16
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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17 mkdir '${out_html.files_path}' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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18 mv plot_*.svg '${out_html.files_path}' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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19
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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20 echo '
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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21 <html><head></head>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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22 <body>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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23 <h1>RaceID k-means</title></h1><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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24 <h3>Gap statistic</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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25 <img src="plot_gap.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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26 <h3>Jaccard Similarity</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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27 <img src="plot_jaccard.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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28 <h3>Silhouette Plot</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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29 <img src="plot_silhouette.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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30 <h3>Cluster Heatmap</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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31 <img src="plot_clustheatmap.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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32 ' > '$out_html' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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33
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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34 ## Outlier -- relies on kmeans
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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35 echo "Outlier" &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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36 Rscript '@SCRIPT_DIR@/raceID_outlierdetect.R' '@SCRIPT_DIR@' '$rconf_source_outlier' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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37
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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38 mv plot_*.svg '${out_html.files_path}' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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39 echo '
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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40 <br/>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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41 <h1>RaceID Outlier Detection</h1><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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42 <h3>Background</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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43 <img src="plot_background.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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44 <h3>Sensitivity</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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45 <img src="plot_sensitivity.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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46 <h3>Outlier Probability</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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47 <img src="plot_outlierprobs.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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48 <h3>Final Heatmap</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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49 <img src="plot_finalheat.svg" ><br />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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50 ' >> '$out_html' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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51
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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52 ## tSNE -- relies on kmeans and outlier
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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53 echo "tSNE" &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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54 Rscript '@SCRIPT_DIR@/raceID_tsne.R' '@SCRIPT_DIR@' '$rconf_source_tsne' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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55
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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56 ##mkdir '${out_html.files_path}' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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57 mv plot_*.svg '${out_html.files_path}' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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58
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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59 echo '
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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60 <br/>
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61 <h1>RaceID tSNE</h1><br />
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62 <h3>Initial k-means clusters</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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63 <br /><img src="plot_initial.svg" >
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64 <h3>Final clusters</h3>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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65 <br /><img src="plot_final.svg" >
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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66 <h3>Labelled</h3>
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67 <br /><img src="plot_labels.svg" >
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68 <h3>Symbols</h3>
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69 <br /><img src="plot_symbols.svg" >
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70 ' >> '$out_html' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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71
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72 #if $section_tsne.genexp_select.use_gexpr == "Yes":
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73 #for $gene_set in $section_tsne.genexp_select.geneset:
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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74 echo "<h3>Expression for: [${gene_set.genes.value}]</h3>" >> '$out_html' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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75 echo "<br /><img src=\"plot_${gene_set.genes.value}\" >" >> '$out_html' &&
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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76 #end for
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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77 #end if
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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78 echo '</body></html>' >> '$out_html'
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79
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80 ]]></command>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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81
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82 <configfiles>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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83 <configfile name="rconf_source_filter">
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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84 count_matrix = '$section_filter.inp_count'
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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85 filtering = as.logical( '$section_filter.filtering.do_filter.value' )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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86 output_table = '$out_table_filter'
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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87 output_rdat = '@out_rdat_filter@'
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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88
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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89 # Defaults
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90 control_genes_filter="";
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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91 c_mintotal = 3000; c_minexpr = 5; c_maxexpr = 500; c_minnumber = 1;
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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92 c_downsample = F; c_dsn = 1; c_rseed = 17000;
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93
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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94 #if $section_filter.filtering.do_filter.value == "T":
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95 control_genes_filter = '$section_filter.filtering.remove_nonendog.value'
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96 #if $section_filter.filtering.default_filtering_select.do_filter_defaults.value == "advanced_options":
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97 c_mintotal = as.integer( '$section_filter.filtering.default_filtering_select.mintotal' )
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98 c_minexpr = as.integer( '$section_filter.filtering.default_filtering_select.minexpr' )
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99 c_maxexpr = as.integer( '$section_filter.filtering.default_filtering_select.maxexpr' )
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100 c_minnumber = as.integer( '$section_filter.filtering.default_filtering_select.minnumber' )
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101 #if $section_filter.filtering.default_filtering_select.dsn:
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102 c_downsample = T;
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103 c_dsn = as.integer( '$section_filter.filtering.default_filtering_select.dsn' )
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104 #end if
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105 c_rseed = as.integer( '$section_filter.filtering.default_filtering_select.filter_rseed' )
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106 #end if
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107 #end if
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108 </configfile>
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109 <configfile name="rconf_source_kmeans">
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110 sc = readRDS( '@inp_rdat_kmeans@' )
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111 output_rdat = '@out_rdat_kmeans@'
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112 c_metric = 'pearson'; c_cln = 0; dogap = T; c_clustnr = 20; bgap = 50;
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113 semethod = 'Tibs2001SEmax'; sefactor = .25; c_bootnr = 50; c_rseed = 17000;
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114
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115 c_metric = '$section_kmeans.metric'
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116 c_cln = as.integer( '$section_kmeans.cln' )
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117 dogap = as.logical( '$section_kmeans.gapstats.dogap.value' )
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118 #if $section_kmeans.gapstats.dogap.value == "T":
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119 c_clustnr = as.integer( '$section_kmeans.gapstats.clustnr' )
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120 bgap = as.integer( '$section_kmeans.gapstats.bgap' )
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iuc
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121 semethod = '$section_kmeans.gapstats.semethod.value'
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iuc
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122 sefactor = as.numeric( '$section_kmeans.gapstats.sefactor' )
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diff changeset
123 #end if
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124 c_bootnr = as.integer( '$section_kmeans.bootnr' )
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125 c_rseed = as.integer( '$section_kmeans.kmeans_rseed' )
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126
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127 generate_final_rdata = T
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128 </configfile>
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129 <configfile name="rconf_source_outlier">
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130 sc = readRDS( '@inp_rdat_outlier@' )
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131 output_rdat = '@out_rdat_outlier@'
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132 output_table= '$out_table_outlier'
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diff changeset
133 # set defaults
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134 c_outminc = 5; c_outlg = 2; c_probthr = 1e-3; c_outdistquant = 0.75;
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135
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136 c_outminc = as.integer( '$section_outlier.outminc' )
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137 c_outlg = as.integer( '$section_outlier.outlg' )
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138 c_probthr = as.numeric( '$section_outlier.probthr' )
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iuc
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diff changeset
139 c_outdistquant = as.numeric( '$section_outlier.probthr' )
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140
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diff changeset
141 generate_final_rdata = T
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diff changeset
142 </configfile>
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143 <configfile name="rconf_source_tsne" >
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144 sc = readRDS( '@inp_rdat_tsne@' )
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iuc
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145 output_rdat = '$out_rdat_tsne' # final output RData
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diff changeset
146 regex_val = ""
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147 c_rseed = '$section_tsne.tsne_rseed'
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148 gene_sets = ""
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149 #if $section_tsne.genexp_select.use_gexpr == 'Yes':
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150 gene_sets = '#for $gns in $section_tsne.genexp_select.geneset# $gns.genes.value _split_ #end for#'
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151 regex_val = '$section_tsne.genexp_select.regex'
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diff changeset
152 #end if
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153 final_rdata = T
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154 </configfile>
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155 </configfiles>
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156 <!-- Filter -->
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diff changeset
157 <inputs>
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158 <section name="section_filter" title="Filtering and Normalisation" expanded="true" >
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159 <param name="inp_count" type="data" format="tsv" label="Count matrix" help="A spreadsheet file with the first row indicating cell IDs, and the first column indicating transcript or gene IDs" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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160 <conditional name="filtering" >
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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161 <param name="do_filter" type="select" label="Perform filtering?" >
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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162 <option value="T" selected="true" >Yes</option>
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163 <option value="F" >No</option>
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diff changeset
164 </param>
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diff changeset
165 <when value="F" />
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diff changeset
166 <when value="T" >
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167 <param name="remove_nonendog" type="text" label="Control gene name prefixes" help="If ERCC or other non-endogenous spike-in RNAs are within the data, please specify their prefixes (e.g. 'ERCC, HK00') in order to filter them out. (Leave blank if control genes were not used in the experiment.)" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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diff changeset
168 <conditional name="default_filtering_select" >
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iuc
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169 <param name="do_filter_defaults" type="select" label="Parameters" >
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170 <option value="use_defaults" selected="true" >Use Defaults</option>
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diff changeset
171 <option value="advanced_options" >Advanced Options</option >
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diff changeset
172 </param>
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iuc
parents:
diff changeset
173 <when value="use_defaults" />
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iuc
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diff changeset
174 <when value="advanced_options" >
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iuc
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175 <param name="mintotal" type="integer" value="3000" min="1" label="Minimum total transcripts" help="Discard cells with less than this number of total transcripts before normalisation." />
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176 <param name="minexpr" type="integer" value="5" min="1" label="Minimum expressed genes" help="Discard genes that do not express a minimum of this number of transcripts after normalisation."/>
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177 <param name="maxexpr" type="integer" value="500" min="0" label="Maximum expressed genes" help="Discard genes that express more than this number of transcripts after normalisation. Useful if genes have oversaturated counts derived from UMI data. Set to 0 to disable this step." />
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178
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179 <param name="minnumber" type="integer" value="1" label="Minimum Cells" help="Discard genes that do not have the minimum expressed transcripts in at least this number of cells" />
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180
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181 <param name="dsn" type="integer" value="1" min="1" optional="true" label="Downsample counts" help="Average transcripts across this many samples. If this is set to 1, then sampling noise should be comparable across cells. For higher values, the data approximates median normalisation." />
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182 <param name="filter_rseed" type="integer" value="17000" min="0" label="Seed value (for reproducibility)" />
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183 </when>
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184 </conditional>
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185 </when>
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186 </conditional>
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187 <param name="filter_table_output" type="boolean" checked="false" label="Generate output table of filtered matrix?" />
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188 </section>
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189
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190 <!-- Kmeans -->
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191 <section name="section_kmeans" title="Clustering (k-means)" expanded="true" >
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192 <param name="metric" type="select" label="Distance metric">
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193 <option value="pearson" selected="true" />
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194 <option value="spearman" />
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195 <option value="kendall" />
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196 <option value="euclidean" />
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197 <option value="maximum" />
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198 <option value="manhattan" />
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199 <option value="canberra" />
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200 <option value="binary" />
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201 <option value="minkowski" />
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202 </param>
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203
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204 <param name="cln" type="integer" value="0" min="0" label="Number of clusters for k-means" help="Leave as zero to automatically determine the number based on gap statistics" />
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205
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206 <conditional name="gapstats">
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207 <param name="dogap" type="select" label="Use gap statistics to determine clusters" >
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208 <option value="T" selected="true" >Yes</option>
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209 <option value="F" >No</option>
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210 </param>
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211
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212 <when value="F" />
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213 <when value="T" >
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214 <param name="clustnr" type="integer" value="2" min="0" label="Maximum number of clusters for the computation of the gap statistic" help="If more major cell types are expected, a higher number than 2 should bde chosen." />
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215 <param name="bgap" type="integer" value="50" min="1" label="Number of bootstraps to run the gap statistic calculation" />
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216 <param name="semethod" type="select" label="Method used for determining first local maximum" >
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217 <option value="Tibs2001SEmax" selected="true" />
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218 <option value="globalmax" />
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219 <option value="firstmax" />
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220 <option value="firstSEmax" />
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221 <option value="globalSEmax" />
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222 </param>
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223
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224 <param name="sefactor" type="float" value="0.25" min="0.0001" max="1" label="Fraction of the standard deviation that the local maximum must differ from neighbouring points." />
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225 </when>
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226 </conditional>
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227
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228 <param name="bootnr" type="integer" value="50" min="1" label="Number of bootstraps for clustering" />
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229 <param name="kmeans_rseed" type="integer" value="17000" min="1" label="Seed value (for reproducibility)" />
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230 </section>
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231 <!-- Outlier -->
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232 <section name="section_outlier" title="Outlier Detection" expanded="true" >
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233 <param name="outminc" type="integer" value="5" min="1" label="Expression cutoff threshold for outlier genes" />
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234 <param name="probthr" type="float" value="1e-3" min="1e-8" max="1" label="Probability threshold of observing a given gene expression level in a cell" help="If lower than this cutoff, the cell is considered an outlier for this gene." />
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235 <param name="outlg" type="integer" value="2" min="1" label="Minimal number of outlier genes required to flag an outlier cells" />
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236 <param name="outdistquant" type="select" label="Merge cells into outlier clusters if their similarity exceeds this quantile in a similarity distribution for all cell pairs" >
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237 <option value="0.25">first (0.25)</option>
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238 <option value="0.50">second (0.50)</option>
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239 <option value="0.75">third (0.75)</option>
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240 </param>
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241 </section>
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242 <section name="section_tsne" title="tSNE plots" expanded="true" >
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243 <!-- tSNE -->
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244 <conditional name="genexp_select" >
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245 <param name="use_gexpr" type="select" label="Highlight the expression of a set of (related) genes over all clusters?" >
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246 <option value="Yes" />
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247 <option value="No" selected="true" />
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248 </param>
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249 <when value="No" />
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250 <when value="Yes" >
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251 <repeat name="geneset" title="Gene sets" >
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252 <param name="genes" type="text" label="Gene(s) of interest" help="e.g. 'Apoa1__chr9+Apoa1bp__chr6'" >
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253 <sanitizer invalid_char="" >
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254 <valid initial="string.letters,string.digits">
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255 <add value="+" /><add value="_" /><add value="-" />
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256 </valid>
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257 </sanitizer>
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258 </param>
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259 </repeat>
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260 <param name="regex" type="text" value="" label="Regular expression to apply over cell labels to identify cell types" help="e.g. for barcodes [ cl_1_ACCAG, cl_1_ACGGA, cl_2_TTAC, ... ] can be grouped into [ cl_1, cl_2, ... ] by the expression: '_[ACTG]+', which removes the last '_' and any following characters belonging to A C T or G." >
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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diff changeset
261 <sanitizer invalid_char="" >
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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262 <valid initial="string.printable" />
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263 </sanitizer>
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264 </param>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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265 </when>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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266 </conditional>
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267 <param name="tsne_rseed" type="integer" min="1" value="15555" label="Seed (for reproducibility)" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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268 </section>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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269 </inputs>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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270
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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271 <outputs>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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diff changeset
272 <!-- Filter -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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273 <data name="out_table_filter" format="tabular" label="${tool.name} on ${on_string}: Filter Table" >
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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274 <filter>section_filter['filtering']['do_filter'] == "T"</filter>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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275 </data>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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276 <!-- Outlier -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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277 <data name="out_table_outlier" format="tabular" label="${tool.name} on ${on_string}: Outliers" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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278 <!-- TSNE -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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279 <data name="out_html" format="html" label="${tool.name} on ${on_string}: Web Report" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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280 <data name="out_rdat_tsne" format="rdata" label="${tool.name} on ${on_string}: tSNE RData" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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281 </outputs>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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282
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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283 <tests>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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284 <!-- vanilla run on all but filter -->
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285 <test>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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286 <!-- Filter -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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287 <param name="inp_count" value="transcript_counts_intestine_sub.tsv" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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288 <!-- These test params are MANDATORY due to the reduced size of the
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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289 input set (due to file size constraints) -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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290 <param name="do_filter" value="T" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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291 <param name="do_filter_defaults" value="advanced_options" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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292 <param name="mintotal" value="10" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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293 <param name="minexpr" value="1" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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294 <param name="maxexpr" value="2000" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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295 <!-- Outlier -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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296 <!-- ... With reduced minc -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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297 <param name="inp_rdat_outlier" value="trans_outlier_in.rds" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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298 <param name="outminc" value="1" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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299 <output name="out_table_outlier" value="out_outlier1.table" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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300 <!-- tSNE -->
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iuc
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301 <output name="out_html" value="out_1.html" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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302 <output name="out_rdat_tsne" value="out_tsne1.rdat" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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303 </test>
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iuc
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diff changeset
304 <!-- manual gap statistics -->
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305 <test>
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
306 <!-- Filter -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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307 <param name="inp_count" value="transcript_counts_intestine_sub.tsv" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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308 <param name="filter_table_output" value="T" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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309 <!-- See message from previous test .. -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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310 <param name="do_filter" value="T" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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311 <param name="do_filter_defaults" value="advanced_options" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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312 <param name="mintotal" value="10" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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313 <param name="minexpr" value="1" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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314 <param name="maxexpr" value="2000" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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315 <output name="out_table_filter" value="out_filter2.table" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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316 <!-- Kmeans -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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317 <!-- ... Auto gap with gap params -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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318 <param name="inp_rdat_kmeans" value="trans_filter_ds.rds" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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319 <param name="clustnr" value="5" />
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iuc
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320 <param name="bgap" value="10" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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321 <param name="semethod" value="globalSEmax" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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322 <param name="sefactor" value="0.6" />
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323 <!-- Outlier -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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324 <!-- ... With reduced minc -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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325 <param name="inp_rdat_outlier" value="trans_outlier_in.rds" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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326 <param name="outminc" value="1" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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327 <output name="out_table_outlier" value="out_outlier2.table" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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328 <!-- tSNE -->
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329 <output name="out_html" value="out_2.html" />
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330 <output name="out_rdat_tsne" value="out_tsne2.rdat" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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331 </test>
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332 <!-- complex run -->
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333 <test>
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334 <!-- Filter -->
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335 <param name="inp_count" value="transcript_counts_intestine_sub.tsv" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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336 <param name="do_filter" value="T" />
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iuc
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337 <param name="do_filter_defaults" value="advanced_options" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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338 <param name="mintotal" value="10" />
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339 <param name="minexpr" value="1" />
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340 <param name="maxexpr" value="2000" />
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341 <param name="dsn" value="3" />
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342 <output name="out_table_filter" value="out_filter3.table" />
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343 <!-- Kmeans -->
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344 <!-- ... Set k-value, no gap, no R obj, metrics and bootrepl. -->
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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345 <param name="inp_rdat_kmeans" value="trans_filter_ds.rds" />
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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346 <param name="metric" value="manhattan" />
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347 <param name="cln" value="6" />
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348 <param name="dogap" value="T" />
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349 <param name="bootnr" value="10" />
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350 <!-- Outlier -->
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351 <!-- ... No R out, other opts-->
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352 <param name="inp_rdat_outlier" value="trans_outlier_in.rds" />
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353 <param name="outminc" value="1" />
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354 <param name="probthr" value="1e-5" />
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355 <param name="outlg" value="10" />
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356 <param name="outdistquant" value="0.50" />
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357 <output name="out_table_outlier" value="out_outlier3.table" />
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358 <!-- tSNE -->
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359 <param name="use_gexpr" value="Yes" />
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360 <repeat name="geneset">
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361 <param name="genes" value="1110007C09Rik__chr13+1110037F02Rik__chr4+1300002K09Rik__chr4" />
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362 </repeat>
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363 <repeat name="geneset">
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364 <param name="genes" value="0610010K14Rik__chr11+1500009L16Rik__chr10" />
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365 </repeat>
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366 <param name="regex" value="[^_]+__" />
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367 <output name="out_html" value="out_3.html" />
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368 <output name="out_rdat_tsne" value="out_tsne3.rdat" />
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369 </test>
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370 </tests>
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371
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372 <help><![CDATA[
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373
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374 ******
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375 RaceID
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376 ******
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377
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378 RaceID(v2) pipeline for scRNA, performs:
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379 * filtering
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380 * normalisation
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381 * k-means clustering
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382 * outlier detection
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383
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384 Generates heatmaps, tSNE plots, and an R object which can be passed into the RaceID DiffGenes tool for expression analysis between different sets of clusters.
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385
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386 **Filtering**
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387
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388 This takes a count matrix/spreadsheet with cellIDs as columns and geneIDs/transcriptIDs as rows, and filters based on standard single-cell RNA pre-processing methods (minimum/maximum transcript expression in a minimum of X number of cells). A filtered matrix is produced as output
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389
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390 **K-means Clustering**
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391
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392 This performs k-means clustering and plots gap statistics, jaccard similarity, silhoutte plots, and preliminary heatmap.
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393
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394 **Outlier Detection**
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395
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396 This performs outlier detection by calibrating against a background noise model within each cluster, and searching for cells that fall outside of the transcript count distribution for that gene (modelled as a negative binomial). Cells that are outliers for more than a user-set amount of genes are suspected as being outlier cells.
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397
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398 **tSNE plots**
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399
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400 Generates multiple tSNE plots with custom expression highlighting for gene subsets of interest. A tSNE map can be drawn for original clusters (derived via k-means) and final clustering (derived from outliers). Any number of genes subsets of interest can be specified to measure expression within clusters for related marker genes or genes characterising a cell type.
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401
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402 ]]></help>
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403 <expand macro="citations" />
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404 </tool>