Mercurial > repos > iuc > raceid_clustering
diff raceid_clustering.xml @ 0:4ea021bd7513 draft
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 |
| parents | |
| children | ee0bbc160cb1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raceid_clustering.xml Thu Nov 22 04:43:57 2018 -0500 @@ -0,0 +1,213 @@ +<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" > + <description>performs clustering, outlier detection, dimensional reduction</description> + <macros> + <import>macros.xml</import> + <import>macros_cluster.xml</import> + </macros> + <expand macro="requirements" /> + <version_command><![CDATA[ +Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@ +]]></version_command> + + <command detect_errors="exit_code"><![CDATA[ +#set bin = 'cluster.R' +Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog' + ]]></command> + + <configfiles> + <configfile name="userconf" ><![CDATA[ +@STRING2VECTOR@ + +@CLUSTER_CHEETAH@ + +]]></configfile> + </configfiles> + <inputs> + <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" /> + <section name="clust" title="Clustering" expanded="true" > + <!-- CompDist --> + <param name="metric" type="select" label="Distance Metric" > + <option value="pearson" selected="true" >Pearson</option> + <option value="spearman">Spearman</option> + <option value="logpearson">Log Pearson</option> + <option value="euclidean">Euclidean</option> + </param> + <!-- ClustExp --> + <param name="funcluster" type="select" label="Clustering method" > + <option value="kmedoids" selected="true" >K-medoids</option> + <option value="kmeans">K-means</option> + <option value="hclust">H-Clust</option> + </param> + <expand macro="use_defaults_no" > + <!-- CompDist --> + <param name="fselect" type="boolean" value="true" label="Perform feature selection" /> + <param name="knn" type="integer" min="0" optional="true" label="KNN" help="Number of nearest neighbours for imputing gene expression" /><!-- 0: NULL --> + <!-- ClustExp --> + <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." /> + <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." /> + <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 --> + <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null --> + <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" /> + <param name="rseed" type="integer" value="17000" label="Random seed" /> + </expand> + </section> + <section name="outlier" title="Outliers" expanded="true" > + <!-- Find Outliers --> + <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" /> + <param name="outlg" type="integer" min="1" value="2" label="Minimum Genes" help="Minimum number of outlier genes required for being an outlier cell" /> + <!-- RFCorrect --> + <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." /> + <expand macro="use_defaults_no" > + <!-- Find Outliers --> + <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" /> + <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" /> + <!-- RFCorrect --> + <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null --> + <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" /> + <param name="rfseed" type="integer" value="12345" label="Random Seed" /> + </expand> + </section> + <section name="tsne" title="tSNE and FR" expanded="true" > + <!-- CompTSNE --> + <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" /> + <!-- CompFR --> + <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" /> + <expand macro="use_defaults_no" > + <!-- CompTSNE --> + <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" /> + <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" /> + <!-- CompFR --> + <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" /> + </expand> + </section> + <section name="extra" title="Extra Parameters" expanded="false" > + <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" /> + <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" /> + <param name="foldchange" type="float" min="0" value="1" label="Fold change" /> + <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" /> + </section> + </inputs> + <outputs> + <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> + <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> + <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" /> + <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > + <filter>use_log</filter> + </data> + </outputs> + + <tests> + <test> + <param name="inputrds" value="matrix.filter.rdat" /> + <output name="outgenelist" value="matrix2.genelist" /> + <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" /> + <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" /> + </test> + <test> + <!-- defaults, but manually specified. No opts, no CC. Generates identical to above --> + <param name="inputrds" value="matrix.filter.rdat" /> + <section name="clust" > + <param name="metric" value="pearson" /> + <param name="funcluster" value="kmedoids" /> + <expand macro="test_nondef" > + <param name="fselect" value="true" /> + <param name="sat" value="true" /> + <param name="clustnr" value="30" /> + <param name="bootnr" value="50" /> + <param name="rseed" value="17000" /> + </expand> + </section> + <section name="outlier" > + <param name="outminc" value="5" /> + <param name="outlg" value="2" /> + <param name="final" value="false" /> + <expand macro="test_nondef" section_name="outlier" > + <param name="probthr" value="0.001" /> + <param name="outdistquant" value="0.95" /> + <param name="rfseed" value="12345" /> + <param name="nbfactor" value="5" /> + </expand> + </section> + <section name="tsne" > + <param name="perplexity" value="30" /> + <param name="knn" value="10" /> + <expand macro="test_nondef" section_name="tsne" > + <param name="initial_cmd" value="true" /> + <param name="rseed_tsne" value="15555" /> + <param name="rfseed_fr" value="15555" /> + </expand> + </section> + <output name="outgenelist" value="intestinal.genelist" /> + <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" /> + </test> + <test> + <!-- Advanced. Opts, CC used --> + <param name="inputrds" value="matrix.filter.rdat" /> + <section name="clust" > + <param name="metric" value="euclidean" /> + <param name="funcluster" value="hclust" /> + <expand macro="test_nondef" > + <param name="fselect" value="false" /> + <param name="knn" value="5" /> + <param name="sat" value="false" /> + <param name="samp" value="10" /> + <param name="cln" value="10" /> + <param name="clustnr" value="10" /> + <param name="bootnr" value="30" /> + <param name="rseed" value="17000" /> + </expand> + </section> + <section name="outlier" > + <param name="outminc" value="3" /> + <param name="outlg" value="5" /> + <param name="final" value="true" /> + <expand macro="test_nondef" > + <param name="probthr" value="0.01" /> + <param name="outdistquant" value="0.5" /> + <param name="rfseed" value="12345" /> + <param name="nbfactor" value="5" /> + <param name="nbtree" value="10" /> + </expand> + </section> + <section name="tsne" > + <param name="perplexity" value="20" /> + <param name="knn" value="6" /> + <expand macro="test_nondef" > + <param name="initial_cmd" value="false" /> + <param name="rseed_tsne" value="15555" /> + <param name="rfseed_fr" value="15555" /> + </expand> + </section> + <output name="outgenelist" value="intestinal_advanced.genelist" /> + <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" /> + </test> + </tests> + <help><![CDATA[ +RaceID3 +========= + +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. + +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). + +The tool generates the following: + + * A list of the most differentially expressed genes in each cluster + * Cluster stability plots: + * 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. + * The point where this flattens out gives you a rough estimate of how many clusters there are in your analysis. + * 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. + * This tells you which genes are the most significant against a background model of random expression. + * A Jaccard stability plot which tells you how well defined your clusters are prior to outlier identification. + * 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. + * Heatmaps: + * The initial and final clustering (as determined using random forest) + * For each of the most differentially expressed genes in each cluster + +The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work. + + +]]> + </help> + <expand macro="citations" /> +</tool>