Mercurial > repos > iuc > raceid_clustering

annotate raceid_clustering.xml @ 4:ee0bbc160cb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author iuc
date Mon, 12 Aug 2019 13:00:12 -0400
parents 4ea021bd7513
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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
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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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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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5 <import>macros_cheetah.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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8 <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&#38;&#62; '$outlog'" />
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9
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10 <inputs>
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11 <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
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12 <section name="clust" title="Clustering" expanded="true" >
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13 <!-- CompDist -->
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14 <param name="metric" type="select" label="Distance Metric" >
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15 <option value="pearson" selected="true" >Pearson</option>
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16 <option value="spearman">Spearman</option>
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17 <option value="logpearson">Log Pearson</option>
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18 <option value="euclidean">Euclidean</option>
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19 </param>
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20 <!-- ClustExp -->
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21 <param name="funcluster" type="select" label="Clustering method" >
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22 <option value="kmedoids" selected="true" >K-medoids</option>
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23 <option value="kmeans">K-means</option>
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24 <option value="hclust">H-Clust</option>
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25 </param>
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26 <expand macro="use_defaults_no" >
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27 <!-- CompDist -->
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28 <param name="fselect" type="boolean" value="true" label="Perform feature selection" />
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29 <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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30 <!-- ClustExp -->
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31 <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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32 <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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33 <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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34 <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null -->
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35 <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" />
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36 <param name="rseed" type="integer" value="17000" label="Random seed" />
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37 </expand>
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38 </section>
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39 <section name="outlier" title="Outliers" expanded="true" >
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40 <!-- Find Outliers -->
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41 <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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42 <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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43 <!-- RFCorrect -->
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44 <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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45 <expand macro="use_defaults_no" >
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46 <!-- Find Outliers -->
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47 <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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48 <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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49 <!-- RFCorrect -->
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50 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
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51 <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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52 <param name="rfseed" type="integer" value="12345" label="Random Seed" />
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53 </expand>
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54 </section>
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55 <section name="tsne" title="tSNE and FR" expanded="true" >
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56 <!-- CompTSNE -->
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57 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
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58 <!-- CompFR -->
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59 <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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60 <expand macro="use_defaults_no" >
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61 <!-- CompTSNE -->
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62 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
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63 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
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64 <!-- CompFR -->
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65 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
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66 </expand>
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67 </section>
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68 <section name="extra" title="Extra Parameters" expanded="false" >
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69 <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" />
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70 <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" />
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71 <param name="foldchange" type="float" min="0" value="1" label="Fold change" />
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72 <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" />
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73 </section>
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74 </inputs>
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75 <outputs>
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76 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
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77 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
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78 <data name="outassignments" format="tabular" label="${tool.name} on ${on_string}: Cell-to-Cluster assignments" />
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79 <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" />
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80 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
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81 <filter>use_log</filter>
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82 </data>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
83 </outputs>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
84 <tests>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
85 <test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
86 <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
87 <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:
diff changeset
88 <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:
diff changeset
89 <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" />
4
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
90 <output name="outassignments" >
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
91 <assert_contents>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
92 <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" />
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
93 </assert_contents>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
94 </output>
0
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 <test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
97 <!-- 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:
diff changeset
98 <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
99 <section name="clust" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
100 <param name="metric" value="pearson" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
101 <param name="funcluster" value="kmedoids" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
102 <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
103 <param name="fselect" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
104 <param name="sat" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
105 <param name="clustnr" value="30" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
106 <param name="bootnr" value="50" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
107 <param name="rseed" value="17000" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
108 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
109 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
110 <section name="outlier" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
111 <param name="outminc" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
112 <param name="outlg" value="2" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
113 <param name="final" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
114 <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:
diff changeset
115 <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:
diff changeset
116 <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:
diff changeset
117 <param name="rfseed" value="12345" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
118 <param name="nbfactor" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
119 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
120 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
121 <section name="tsne" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
122 <param name="perplexity" value="30" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
123 <param name="knn" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
124 <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:
diff changeset
125 <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:
diff changeset
126 <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:
diff changeset
127 <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
128 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
129 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
130 <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:
diff changeset
131 <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
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diff changeset
132 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
133 <test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
134 <!-- 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
135 <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
136 <section name="clust" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
137 <param name="metric" value="euclidean" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
138 <param name="funcluster" value="hclust" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
139 <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
140 <param name="fselect" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
141 <param name="knn" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
142 <param name="sat" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
143 <param name="samp" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
144 <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
145 <param name="clustnr" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
146 <param name="bootnr" value="30" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
147 <param name="rseed" value="17000" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
148 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
149 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
150 <section name="outlier" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
151 <param name="outminc" value="3" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
152 <param name="outlg" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
153 <param name="final" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
154 <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
155 <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:
diff changeset
156 <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:
diff changeset
157 <param name="rfseed" value="12345" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
158 <param name="nbfactor" value="5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
159 <param name="nbtree" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
160 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
161 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
162 <section name="tsne" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
163 <param name="perplexity" value="20" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
164 <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
165 <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
166 <param name="initial_cmd" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
167 <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:
diff changeset
168 <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
169 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
170 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
171 <output name="outgenelist" value="intestinal_advanced.genelist" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
172 <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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173 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
174 </tests>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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175 <help><![CDATA[
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176 RaceID3
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177 =========
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178
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179 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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180
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181 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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182
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183 The tool generates the following:
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184
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185 * A list of the most differentially expressed genes in each cluster
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186 * Cluster stability plots:
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187 * 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.
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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188 * The point where this flattens out gives you a rough estimate of how many clusters there are in your analysis.
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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189 * 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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190 * This tells you which genes are the most significant against a background model of random expression.
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191 * A Jaccard stability plot which tells you how well defined your clusters are prior to outlier identification.
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192 * 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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193 * Heatmaps:
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194 * The initial and final clustering (as determined using random forest)
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195 * For each of the most differentially expressed genes in each cluster
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196
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197 The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work.
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198
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199
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200 ]]>
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201 </help>
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202 <expand macro="citations" />
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203 </tool>