Mercurial > repos > iuc > raceid_clustering

annotate raceid_clustering.xml @ 0:4ea021bd7513 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author iuc
date Thu, 22 Nov 2018 04:43:57 -0500
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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2 <description>performs clustering, outlier detection, dimensional reduction</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_cluster.xml</import>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command><![CDATA[
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9 Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
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10 ]]></version_command>
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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12 <command detect_errors="exit_code"><![CDATA[
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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13 #set bin = 'cluster.R'
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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14 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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15 ]]></command>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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17 <configfiles>
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18 <configfile name="userconf" ><![CDATA[
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19 @STRING2VECTOR@
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21 @CLUSTER_CHEETAH@
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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23 ]]></configfile>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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24 </configfiles>
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25 <inputs>
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26 <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
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27 <section name="clust" title="Clustering" expanded="true" >
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28 <!-- CompDist -->
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29 <param name="metric" type="select" label="Distance Metric" >
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30 <option value="pearson" selected="true" >Pearson</option>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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31 <option value="spearman">Spearman</option>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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32 <option value="logpearson">Log Pearson</option>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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33 <option value="euclidean">Euclidean</option>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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34 </param>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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35 <!-- ClustExp -->
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36 <param name="funcluster" type="select" label="Clustering method" >
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37 <option value="kmedoids" selected="true" >K-medoids</option>
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38 <option value="kmeans">K-means</option>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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39 <option value="hclust">H-Clust</option>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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40 </param>
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41 <expand macro="use_defaults_no" >
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42 <!-- CompDist -->
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43 <param name="fselect" type="boolean" value="true" label="Perform feature selection" />
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44 <param name="knn" type="integer" min="0" optional="true" label="KNN" help="Number of nearest neighbours for imputing gene expression" /><!-- 0: NULL -->
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45 <!-- ClustExp -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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46 <param name="sat" type="boolean" checked="true" label="Saturation-based clustering?" help="Determine number of clusters on saturation point of the mean within-cluster dispersion as a function of the cluster number." />
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47 <param name="clustnr" type="integer" min="0" value="30" label="Max number of clusters using Saturation-by-mean" help="Max number of clusters for the derivation of the cluster number by the saturation of mean within-cluster-dispersion." />
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48 <param name="samp" type="integer" min="0" optional="true" label="Sample random number of cells" help="Number of random sample of cells used for the inference of cluster number and Jaccard similarity" /><!-- 0:NULL -->
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49 <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null -->
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50 <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" />
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51 <param name="rseed" type="integer" value="17000" label="Random seed" />
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52 </expand>
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53 </section>
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54 <section name="outlier" title="Outliers" expanded="true" >
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55 <!-- Find Outliers -->
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56 <param name="outminc" type="integer" min="0" value="5" label="Minimum Transcripts" help="minimal transcript count of a gene in a clusters to be tested for being an outlier gene" />
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57 <param name="outlg" type="integer" min="1" value="2" label="Minimum Genes" help="Minimum number of outlier genes required for being an outlier cell" />
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58 <!-- RFCorrect -->
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59 <param name="final" type="boolean" value="true" label="Plot Final Clusters?" help="Reclassification of cell types using out-of-bag analysis is performed based on the final clusters after outlier identification. If 'FALSE', then the cluster partition prior to outlier identification is used for reclassification." />
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60 <expand macro="use_defaults_no" >
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61 <!-- Find Outliers -->
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62 <param name="probthr" type="float" min="0" value="0.001" label="Outlier Probability Threshold" help="Probability threshold for the above specified minimum number of genes to be an outlier cell. This probability is computed from a negative binomial background model of expression in a cluster" />
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63 <param name="outdistquant" type="float" min="0" max="1" value="0.95" label="Outlier Distance Quantile" help="Outlier cells are merged to outlier clusters if their distance smaller than the outdistquant-quantile of the distance distribution of pairs of cells in the orginal clusters after outlier removal" />
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64 <!-- RFCorrect -->
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65 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
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66 <param name="nbfactor" type="integer" min="0" value="5" label="Tree Factor" help="Number of trees based on the number of cells multiplied by this factor. Effective only if the number of trees parameter is set to 0" />
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67 <param name="rfseed" type="integer" value="12345" label="Random Seed" />
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68 </expand>
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69 </section>
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70 <section name="tsne" title="tSNE and FR" expanded="true" >
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71 <!-- CompTSNE -->
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72 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
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73 <!-- CompFR -->
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74 <param name="knn" type="integer" min="0" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" />
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75 <expand macro="use_defaults_no" >
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76 <!-- CompTSNE -->
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77 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
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78 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
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79 <!-- CompFR -->
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80 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
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81 </expand>
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82 </section>
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83 <section name="extra" title="Extra Parameters" expanded="false" >
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84 <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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85 <param name="plotlim" type="integer" min="1" value="10" label="Plot Limit" help="Top N genes to plot. Must be less than or equal to the Table Limit" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
86 <param name="foldchange" type="float" min="0" value="1" label="Fold change" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
87 <param name="pvalue" type="float" min="0" max="1" value="0.01" label="P-value Cutoff" help="P-value cutoff for the inference of differential gene expression" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
88 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
89 </inputs>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
90 <outputs>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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91 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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92 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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94 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 <filter>use_log</filter>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 </data>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
97 </outputs>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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98
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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99 <tests>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
100 <test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
101 <param name="inputrds" value="matrix.filter.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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102 <output name="outgenelist" value="matrix2.genelist" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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103 <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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104 <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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105 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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106 <test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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107 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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108 <param name="inputrds" value="matrix.filter.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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109 <section name="clust" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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110 <param name="metric" value="pearson" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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111 <param name="funcluster" value="kmedoids" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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112 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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113 <param name="fselect" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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114 <param name="sat" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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115 <param name="clustnr" value="30" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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116 <param name="bootnr" value="50" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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117 <param name="rseed" value="17000" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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118 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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119 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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120 <section name="outlier" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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121 <param name="outminc" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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122 <param name="outlg" value="2" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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123 <param name="final" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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124 <expand macro="test_nondef" section_name="outlier" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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125 <param name="probthr" value="0.001" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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126 <param name="outdistquant" value="0.95" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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127 <param name="rfseed" value="12345" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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128 <param name="nbfactor" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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129 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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130 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
131 <section name="tsne" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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132 <param name="perplexity" value="30" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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133 <param name="knn" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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134 <expand macro="test_nondef" section_name="tsne" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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135 <param name="initial_cmd" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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136 <param name="rseed_tsne" value="15555" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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137 <param name="rfseed_fr" value="15555" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
138 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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139 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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140 <output name="outgenelist" value="intestinal.genelist" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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141 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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142 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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143 <test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
144 <!-- Advanced. Opts, CC used -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
145 <param name="inputrds" value="matrix.filter.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
146 <section name="clust" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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147 <param name="metric" value="euclidean" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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148 <param name="funcluster" value="hclust" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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149 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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150 <param name="fselect" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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151 <param name="knn" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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152 <param name="sat" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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153 <param name="samp" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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154 <param name="cln" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
155 <param name="clustnr" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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156 <param name="bootnr" value="30" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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157 <param name="rseed" value="17000" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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158 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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159 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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160 <section name="outlier" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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161 <param name="outminc" value="3" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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162 <param name="outlg" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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163 <param name="final" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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164 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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165 <param name="probthr" value="0.01" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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166 <param name="outdistquant" value="0.5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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167 <param name="rfseed" value="12345" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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168 <param name="nbfactor" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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169 <param name="nbtree" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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170 </expand>
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iuc
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171 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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172 <section name="tsne" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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173 <param name="perplexity" value="20" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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174 <param name="knn" value="6" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
175 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
176 <param name="initial_cmd" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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177 <param name="rseed_tsne" value="15555" />
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178 <param name="rfseed_fr" value="15555" />
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179 </expand>
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180 </section>
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181 <output name="outgenelist" value="intestinal_advanced.genelist" />
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182 <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
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183 </test>
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184 </tests>
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185 <help><![CDATA[
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186 RaceID3
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187 =========
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188
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189 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.
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190
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191 This module performs clustering, and outlier detection and ultimately tells you how well defined your clusters are (even if the resultant tSNE plots look messy).
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192
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193 The tool generates the following:
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194
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195 * A list of the most differentially expressed genes in each cluster
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196 * Cluster stability plots:
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197 * The mean within-cluster dispersion as a function of the cluster number and highlights the saturation point inferred based on the saturation criterion applied by RaceID3. The number of clusters where the change in within-cluster dispersion upon adding further clusters approaches linear behaviour demarcates the saturation point is highlighted in blue.
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198 * The point where this flattens out gives you a rough estimate of how many clusters there are in your analysis.
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199 * A scatter plot showing the gene expression variance as a function of the mean and the inferred polynomial fit of the background model, as well as a local regression.
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200 * This tells you which genes are the most significant against a background model of random expression.
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201 * A Jaccard stability plot which tells you how well defined your clusters are prior to outlier identification.
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202 * Good stable clusters should near the 0.8 mark, but 0.6 is acceptable, and for a large number of clusters, one or two low scoring clusters are also acceptable.
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203 * Heatmaps:
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204 * The initial and final clustering (as determined using random forest)
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205 * For each of the most differentially expressed genes in each cluster
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206
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207 The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work.
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208
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209
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210 ]]>
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211 </help>
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212 <expand macro="citations" />
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213 </tool>