raceid_inspecttrajectory: macros

annotate macros_cluster.xml @ 0:e0e9b24d76aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138

author	iuc
date	Thu, 22 Nov 2018 04:42:18 -0500
parents
children	4164c0da0a5d

rev	line source
0 e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	1 <macros>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	2 <macro name="cluster_inputs" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	3 <param name="intable" type="data" format="tabular" label="Count Matrix" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	4 <section name="filt" title="Filtering" expanded="true" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	5 <param name="mintotal" type="integer" min="1" value="3000" label="Min Transcripts" help="The minimum total transcripts required. Cells with less than mintotal transcripts are filtered out." />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	6 <param name="minexpr" type="integer" min="1" value="5" label="Min Expression" help="The minimum required transcript counts of a gene in the minimum number of cells (below)" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	7 <param name="minnumber" type="integer" min="1" value="5" label="Min Cells" help="The minumum number of cells for gene expression to be counted" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	8 <expand macro="use_defaults_no" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	9 <param name="knn" type="integer" min="0" value="10" label="K-nearest-neighbours" help="Number of nearest neighbors used to infer corresponding cell types in different batches" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	10 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	11 <expand macro="sanitize_string_vector" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	12 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	13 <param name="FGenes" type="text" optional="true" label="FGenes" help="Explicitly filter out genes for cell type inference" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	14 <expand macro="sanitize_string_vector" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	15 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	16 <param name="LBatch_regexes" type="text" optional="true" label="Batch Regex" help="List of regexes to capture experimental batches for batch effect correction" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	17 <expand macro="sanitize_string_vector" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	18 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	19 <param name="ccor" type="float" value="0.4" label="CCor" help="Correlation coefficient used as a threshold for determining correlated genes" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	20 <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	21 <option value="RaceID" selected="true" >RaceID</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	22 <option value="scran">SCRAN</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	23 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	24 <conditional name="ccc" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	25 <param name="use" type="select" label="Perform Cell-cycle correction?" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	26 <option value="yes" >Yes</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	27 <option value="no" selected="true" >No</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	28 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	29 <when value="no" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	30 <when value="yes" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	31 <param name="vset" type="text" optional="true" label="List of Gene Sets" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	32 <expand macro="sanitize_string_vector" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	33 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	34 <param name="pvalue" type="float" value="0.01" min="0" max="1" label="P-value Cutoff" help="P-value cutoff for determining enriched components" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	35 <param name="quant" type="float" value="0.01" min="0" max="1" label="Quantification Fraction" help="Upper and lower fraction of gene loadings use for determining enriched components" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	36 <param name="ncomp" type="integer" min="0" optional="true" label="Number of components to use" help="If left blank, the maximum number of components are used" /><!-- 0 = NULL -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	37 <param name="dimr" type="boolean" value="true" label="Derive Components from saturation criterion" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	38 <param name="mode" type="select" label="Type of Component Analysis" help="If ICA is selected, ensure that the number of components value above is sufficiently high" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	39 <option value="pca" selected="true">PCA</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	40 <option value="ica">ICA</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	41 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	42 <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	43 </when>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	44 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	45 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	46 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	47 <section name="clust" title="Clustering" expanded="true" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	48 <!-- CompDist -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	49 <param name="metric" type="select" label="Distance Metric" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	50 <option value="pearson" selected="true" >Pearson</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	51 <option value="spearman">Spearman</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	52 <option value="logpearson">Log Pearson</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	53 <option value="euclidean">Euclidean</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	54 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	55 <!-- ClustExp -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	56 <param name="funcluster" type="select" label="Clustering method" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	57 <option value="kmedoids" selected="true" >K-medoids</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	58 <option value="kmeans">K-means</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	59 <option value="hclust">H-Clust</option>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	60 </param>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	61 <expand macro="use_defaults_no" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	62 <!-- CompDist -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	63 <param name="fselect" type="boolean" value="true" label="Perform feature selection" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	64 <param name="knn" type="integer" min="0" optional="true" label="KNN" help="Number of nearest neighbours for imputing gene expression" /><!-- 0: NULL -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	65 <!-- ClustExp -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	66 <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." />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	67 <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." />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	68 <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 -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	69 <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	70 <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	71 <param name="rseed" type="integer" value="17000" label="Random seed" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	72 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	73 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	74 <section name="outlier" title="Outliers" expanded="true" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	75 <!-- Find Outliers -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	76 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	77 <param name="outlg" type="integer" min="1" value="2" label="Minimum Genes" help="Minimum number of outlier genes required for being an outlier cell" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	78 <!-- RFCorrect -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	79 <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." />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	80 <expand macro="use_defaults_no" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	81 <!-- Find Outliers -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	82 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	83 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	84 <!-- RFCorrect -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	85 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	86 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	87 <param name="rfseed" type="integer" value="12345" label="Random Seed" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	88 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	89 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	90 <section name="tsne" title="tSNE and FR" expanded="true" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	91 <!-- CompTSNE -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	92 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	93 <!-- CompFR -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	94 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	95 <expand macro="use_defaults_no" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	96 <!-- CompTSNE -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	97 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	98 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	99 <!-- CompFR -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	100 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	101 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	102 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	103 <section name="extra" title="Extra Parameters" expanded="false" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	104 <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	105 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	106 <param name="foldchange" type="float" min="0" value="1" label="Fold change" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	107 <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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	108 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	109 </macro>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	110 <macro name="cluster_tests" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	111 <test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	112 <!-- default test -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	113 <conditional name="tool" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	114 <param name="mode" value="cluster" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	115 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	116 <param name="intable" value="use.intestinal" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	117 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	118 <output name="outgenelist" value="intestinal.genelist" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	119 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	120 </test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	121 <test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	122 <!-- defaults, feeding in a matrix with reduced filtering -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	123 <conditional name="tool" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	124 <param name="mode" value="cluster" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	125 <param name="intable" value="matrix.tabular" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	126 <section name="filt" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	127 <param name="mintotal" value="1000" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	128 <param name="minexpr" value="1" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	129 <param name="minnumber" value="3" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	130 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	131 <param name="use_log" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	132 <output name="outgenelist" value="matrix.genelist" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	133 <output name="outrdat" value="matrix.rdat" compare="sim_size" delta="15" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	134 <output name="outpdf" value="matrix.pdf" compare="sim_size" delta="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	135 <output name="outlog" value="matrix.log" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	136 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	137 </test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	138 <test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	139 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	140 <conditional name="tool" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	141 <param name="mode" value="cluster" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	142 <param name="intable" value="use.intestinal" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	143 <section name="filt" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	144 <param name="mintotal" value="3000" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	145 <param name="minexpr" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	146 <param name="minnumber" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	147 <expand macro="test_nondef" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	148 <param name="knn" value="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	149 <param name="ccor" value="0.4" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	150 <param name="bmode" value="RaceID" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	151 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	152 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	153 <section name="clust" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	154 <param name="metric" value="pearson" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	155 <param name="funcluster" value="kmedoids" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	156 <expand macro="test_nondef" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	157 <param name="fselect" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	158 <param name="sat" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	159 <param name="clustnr" value="30" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	160 <param name="bootnr" value="50" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	161 <param name="rseed" value="17000" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	162 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	163 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	164 <section name="outlier" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	165 <param name="outminc" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	166 <param name="outlg" value="2" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	167 <param name="final" value="false" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	168 <expand macro="test_nondef" section_name="outlier" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	169 <param name="probthr" value="0.001" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	170 <param name="outdistquant" value="0.95" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	171 <param name="rfseed" value="12345" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	172 <param name="nbfactor" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	173 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	174 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	175 <section name="tsne" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	176 <param name="perplexity" value="30" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	177 <param name="knn" value="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	178 <expand macro="test_nondef" section_name="tsne" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	179 <param name="initial_cmd" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	180 <param name="rseed_tsne" value="15555" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	181 <param name="rfseed_fr" value="15555" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	182 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	183 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	184 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	185 <output name="outgenelist" value="intestinal.genelist" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	186 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	187 </test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	188 <test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	189 <!-- Advanced. Opts, CC used -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	190 <conditional name="tool" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	191 <param name="mode" value="cluster" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	192 <param name="intable" value="use.intestinal" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	193 <section name="filt" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	194 <param name="mintotal" value="2000" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	195 <param name="minexpr" value="3" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	196 <param name="minnumber" value="2" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	197 <expand macro="test_nondef" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	198 <param name="knn" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	199 <param name="ccor" value="0.5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	200 <param name="CGenes" value="Gga3,Ggact,Ggct" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	201 <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	202 <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	203 <param name="bmode" value="scran" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	204 <conditional name="ccc" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	205 <param name="use" value="yes" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	206 <param name="pvalue" value="0.05" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	207 <param name="quant" value="0.05" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	208 <param name="ncomp" value="3" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	209 <param name="dimr" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	210 <param name="mode" value="pca" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	211 <param name="logscale" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	212 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	213 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	214 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	215 <section name="clust" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	216 <param name="metric" value="euclidean" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	217 <param name="funcluster" value="hclust" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	218 <expand macro="test_nondef" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	219 <param name="fselect" value="false" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	220 <param name="knn" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	221 <param name="sat" value="false" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	222 <param name="samp" value="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	223 <param name="cln" value="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	224 <param name="clustnr" value="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	225 <param name="bootnr" value="30" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	226 <param name="rseed" value="17000" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	227 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	228 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	229 <section name="outlier" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	230 <param name="outminc" value="3" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	231 <param name="outlg" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	232 <param name="final" value="true" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	233 <expand macro="test_nondef" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	234 <param name="probthr" value="0.01" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	235 <param name="outdistquant" value="0.5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	236 <param name="rfseed" value="12345" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	237 <param name="nbfactor" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	238 <param name="nbtree" value="10" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	239 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	240 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	241 <section name="tsne" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	242 <param name="perplexity" value="20" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	243 <param name="knn" value="6" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	244 <expand macro="test_nondef" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	245 <param name="initial_cmd" value="false" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	246 <param name="rseed_tsne" value="15555" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	247 <param name="rfseed_fr" value="15555" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	248 </expand>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	249 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	250 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	251 <output name="outgenelist" value="intestinal_advanced.genelist" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	252 <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	253 </test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	254 </macro>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	255 <token name="@FILTNORM_CHEETAH@"><![CDATA[
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	256 ## Perform do.filter
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	257 use.filtnormconf = TRUE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	258
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	259 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	260 use.cluster = FALSE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	261
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	262 in.table = read.table(
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	263 '${intable}',
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	264 stringsAsFactors = F,
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	265 na.strings=c("NA", "-", "?", "."),
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	266 sep='\t',
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	267 header=TRUE,
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	268 row.names=1
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	269 )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	270
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	271 ## Hidden flag to use test data instead
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	272 ## see: test-data/use.intestinal
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	273
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	274 use.test.data = (names(in.table)[1] == "test")
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	275
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	276 sc = NULL
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	277 if (use.test.data) {
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	278 sc = SCseq(intestinalData)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	279 message("Loading test data from library")
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	280 } else {
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	281 sc = SCseq(in.table)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	282 }
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	283
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	284
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	285 filt = formals(filterdata)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	286 filt.ccc = formals(CCcorrect)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	287 filt.use.ccorrect = FALSE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	288 filt.lbatch.regexes = NULL
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	289
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	290 filt\$mintotal = as.integer( '$filt.mintotal' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	291 filt\$minexpr = as.integer( '$filt.minexpr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	292 filt\$minnumber = as.integer( '$filt.minnumber' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	293 #if str($filt.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	294 filt\$knn = as.integer( '$filt.use.knn' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	295 filt\$ccor = as.numeric( '$filt.use.ccor' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	296 filt\$bmode = as.character( '$filt.use.bmode' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	297 #if $filt.use.LBatch_regexes:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	298 filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	299 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	300 #if $filt.use.CGenes:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	301 filt\$CGenes = string2textvector( '$filt.use.CGenes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	302 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	303 #if $filt.use.FGenes:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	304 filt\$FGenes = string2textvector( '$filt.use.FGenes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	305 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	306 #if str($filt.use.ccc.use) == "yes"
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	307 filt.use.ccorrect = TRUE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	308 #if $filt.use.ccc.vset:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	309 filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	310 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	311 #if $filt.use.ccc.ncomp:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	312 filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	313 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	314 filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	315 filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	316 filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	317 filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	318 filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	319 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	320 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	321
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	322 out.pdf = '${outpdf}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	323 out.rdat = '${outrdat}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	324
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	325 ]]></token>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	326 <token name="@CLUSTER_CHEETAH@"><![CDATA[
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	327
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	328 in.rdat = readRDS('${inputrds}')
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	329
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	330 sc = in.rdat
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	331
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	332 ## Perform do.filter
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	333 use.filtnormconf = FALSE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	334
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	335 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	336 use.cluster = TRUE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	337
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	338
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	339 clust.compdist = formals(compdist)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	340 clust.clustexp = formals(clustexp)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	341 clust.compdist\$metric = as.character( '$clust.metric' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	342 clust.clustexp\$FUNcluster = as.character( '$clust.funcluster' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	343
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	344 #if str($clust.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	345
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	346 clust.compdist\$FSelect = as.logical( '$clust.use.fselect' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	347 #if $clust.use.knn:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	348 clust.compdist\$knn = as.integer( '$clust.use.knn' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	349 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	350 clust.clustexp\$sat = as.logical( '$clust.use.sat' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	351 #if $clust.use.samp:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	352 clust.clustexp\$samp = as.integer( '$clust.use.samp' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	353 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	354 #if $clust.use.cln:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	355 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	356 clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	357 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	358 ##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	359 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	360 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	361
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	362 outlier.use.randomforest = FALSE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	363 outlier.findoutliers = formals(findoutliers)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	364 outlier.clustheatmap = formals(clustheatmap)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	365 outlier.rfcorrect = formals(rfcorrect)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	366
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	367 outlier.findoutliers\$outminc = as.integer( '$outlier.outminc' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	368 outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	369 outlier.rfcorrect\$final = as.logical( '$outlier.final' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	370
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	371 #if str($outlier.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	372 #if $outlier.use.nbtree:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	373 outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	374 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	375 outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	376 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	377 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	378 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	379 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	380
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	381 cluster.comptsne = formals(comptsne)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	382 cluster.compfr = formals(compfr)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	383
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	384 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	385 cluster.compfr\$knn = as.integer( '$tsne.knn' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	386 #if str($tsne.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	387 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	388 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	389 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	390 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	391
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	392 genelist.tablelim = as.integer( '$extra.tablelim' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	393 genelist.plotlim = as.integer( '$extra.plotlim' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	394 genelist.foldchange = as.integer( '$extra.foldchange' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	395 genelist.pvalue = as.numeric( '$extra.pvalue' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	396
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	397 out.pdf = '${outpdf}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	398 out.rdat = '${outrdat}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	399 out.genelist = '${outgenelist}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	400
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	401 ]]>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	402 </token>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138 iuc parents: diff changeset	403 </macros>

Mercurial > repos > iuc > raceid_inspecttrajectory

annotate macros_cluster.xml @ 0:e0e9b24d76aa draft