Mercurial > repos > iuc > raceid_inspecttrajectory

annotate macros_cluster.xml @ 1:7967b3d036d1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6
author iuc
date Thu, 28 Feb 2019 12:58:58 -0500
parents e0e9b24d76aa
children 4164c0da0a5d
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e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <macros>
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2 <macro name="cluster_inputs" >
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3 <param name="intable" type="data" format="tabular" label="Count Matrix" />
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4 <section name="filt" title="Filtering" expanded="true" >
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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." />
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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)" />
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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" />
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8 <expand macro="use_defaults_no" >
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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" />
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10 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
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11 <expand macro="sanitize_string_vector" />
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12 </param>
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13 <param name="FGenes" type="text" optional="true" label="FGenes" help="Explicitly filter out genes for cell type inference" >
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14 <expand macro="sanitize_string_vector" />
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15 </param>
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16 <param name="LBatch_regexes" type="text" optional="true" label="Batch Regex" help="List of regexes to capture experimental batches for batch effect correction" >
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17 <expand macro="sanitize_string_vector" />
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18 </param>
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19 <param name="ccor" type="float" value="0.4" label="CCor" help="Correlation coefficient used as a threshold for determining correlated genes" />
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20 <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" >
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21 <option value="RaceID" selected="true" >RaceID</option>
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22 <option value="scran">SCRAN</option>
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23 </param>
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24 <conditional name="ccc" >
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25 <param name="use" type="select" label="Perform Cell-cycle correction?" >
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26 <option value="yes" >Yes</option>
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27 <option value="no" selected="true" >No</option>
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28 </param>
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29 <when value="no" />
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30 <when value="yes" >
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31 <param name="vset" type="text" optional="true" label="List of Gene Sets" >
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32 <expand macro="sanitize_string_vector" />
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33 </param>
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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" />
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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" />
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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 -->
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37 <param name="dimr" type="boolean" value="true" label="Derive Components from saturation criterion" />
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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" >
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39 <option value="pca" selected="true">PCA</option>
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40 <option value="ica">ICA</option>
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41 </param>
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42 <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
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43 </when>
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44 </conditional>
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45 </expand>
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46 </section>
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47 <section name="clust" title="Clustering" expanded="true" >
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48 <!-- CompDist -->
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49 <param name="metric" type="select" label="Distance Metric" >
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50 <option value="pearson" selected="true" >Pearson</option>
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51 <option value="spearman">Spearman</option>
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52 <option value="logpearson">Log Pearson</option>
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53 <option value="euclidean">Euclidean</option>
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54 </param>
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55 <!-- ClustExp -->
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56 <param name="funcluster" type="select" label="Clustering method" >
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57 <option value="kmedoids" selected="true" >K-medoids</option>
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58 <option value="kmeans">K-means</option>
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59 <option value="hclust">H-Clust</option>
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60 </param>
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61 <expand macro="use_defaults_no" >
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62 <!-- CompDist -->
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63 <param name="fselect" type="boolean" value="true" label="Perform feature selection" />
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64 <param name="knn" type="integer" min="0" optional="true" label="KNN" help="Number of nearest neighbours for imputing gene expression" /><!-- 0: NULL -->
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65 <!-- ClustExp -->
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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." />
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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." />
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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 -->
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69 <param name="cln" type="integer" min="0" optional="true" label="Number of clusters" /><!-- 0:Null -->
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70 <param name="bootnr" type="integer" min="0" value="50" label="Number of booststrapping runs" />
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71 <param name="rseed" type="integer" value="17000" label="Random seed" />
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72 </expand>
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73 </section>
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74 <section name="outlier" title="Outliers" expanded="true" >
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75 <!-- Find Outliers -->
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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" />
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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" />
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78 <!-- RFCorrect -->
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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." />
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80 <expand macro="use_defaults_no" >
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81 <!-- Find Outliers -->
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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" />
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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" />
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84 <!-- RFCorrect -->
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85 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
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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" />
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87 <param name="rfseed" type="integer" value="12345" label="Random Seed" />
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88 </expand>
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89 </section>
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90 <section name="tsne" title="tSNE and FR" expanded="true" >
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91 <!-- CompTSNE -->
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92 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
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93 <!-- CompFR -->
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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" />
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95 <expand macro="use_defaults_no" >
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96 <!-- CompTSNE -->
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97 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
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98 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
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99 <!-- CompFR -->
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100 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
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101 </expand>
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102 </section>
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103 <section name="extra" title="Extra Parameters" expanded="false" >
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104 <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" />
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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" />
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106 <param name="foldchange" type="float" min="0" value="1" label="Fold change" />
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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" />
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108 </section>
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109 </macro>
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110 <macro name="cluster_tests" >
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111 <test>
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112 <!-- default test -->
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113 <conditional name="tool" >
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114 <param name="mode" value="cluster" />
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115 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
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116 <param name="intable" value="use.intestinal" />
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117 </conditional>
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118 <output name="outgenelist" value="intestinal.genelist" />
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119 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
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120 </test>
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121 <test>
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122 <!-- defaults, feeding in a matrix with reduced filtering -->
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123 <conditional name="tool" >
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124 <param name="mode" value="cluster" />
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125 <param name="intable" value="matrix.tabular" />
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126 <section name="filt" >
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127 <param name="mintotal" value="1000" />
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128 <param name="minexpr" value="1" />
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129 <param name="minnumber" value="3" />
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130 </section>
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131 <param name="use_log" value="true" />
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132 <output name="outgenelist" value="matrix.genelist" />
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133 <output name="outrdat" value="matrix.rdat" compare="sim_size" delta="15" />
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134 <output name="outpdf" value="matrix.pdf" compare="sim_size" delta="10" />
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135 <output name="outlog" value="matrix.log" />
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136 </conditional>
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137 </test>
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138 <test>
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139 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
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140 <conditional name="tool" >
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141 <param name="mode" value="cluster" />
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142 <param name="intable" value="use.intestinal" />
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143 <section name="filt" >
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144 <param name="mintotal" value="3000" />
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145 <param name="minexpr" value="5" />
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146 <param name="minnumber" value="5" />
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147 <expand macro="test_nondef" >
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148 <param name="knn" value="10" />
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149 <param name="ccor" value="0.4" />
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150 <param name="bmode" value="RaceID" />
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151 </expand>
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152 </section>
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153 <section name="clust" >
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154 <param name="metric" value="pearson" />
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155 <param name="funcluster" value="kmedoids" />
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156 <expand macro="test_nondef" >
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157 <param name="fselect" value="true" />
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158 <param name="sat" value="true" />
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159 <param name="clustnr" value="30" />
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160 <param name="bootnr" value="50" />
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161 <param name="rseed" value="17000" />
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162 </expand>
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163 </section>
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164 <section name="outlier" >
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165 <param name="outminc" value="5" />
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166 <param name="outlg" value="2" />
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167 <param name="final" value="false" />
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168 <expand macro="test_nondef" section_name="outlier" >
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169 <param name="probthr" value="0.001" />
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170 <param name="outdistquant" value="0.95" />
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171 <param name="rfseed" value="12345" />
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172 <param name="nbfactor" value="5" />
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173 </expand>
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174 </section>
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175 <section name="tsne" >
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176 <param name="perplexity" value="30" />
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177 <param name="knn" value="10" />
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178 <expand macro="test_nondef" section_name="tsne" >
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179 <param name="initial_cmd" value="true" />
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180 <param name="rseed_tsne" value="15555" />
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181 <param name="rfseed_fr" value="15555" />
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182 </expand>
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183 </section>
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184 </conditional>
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185 <output name="outgenelist" value="intestinal.genelist" />
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186 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
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187 </test>
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188 <test>
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189 <!-- Advanced. Opts, CC used -->
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190 <conditional name="tool" >
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191 <param name="mode" value="cluster" />
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192 <param name="intable" value="use.intestinal" />
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193 <section name="filt" >
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194 <param name="mintotal" value="2000" />
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195 <param name="minexpr" value="3" />
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196 <param name="minnumber" value="2" />
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197 <expand macro="test_nondef" >
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198 <param name="knn" value="5" />
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199 <param name="ccor" value="0.5" />
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200 <param name="CGenes" value="Gga3,Ggact,Ggct" />
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iuc
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201 <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" />
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202 <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" />
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203 <param name="bmode" value="scran" />
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204 <conditional name="ccc" >
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205 <param name="use" value="yes" />
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206 <param name="pvalue" value="0.05" />
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207 <param name="quant" value="0.05" />
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208 <param name="ncomp" value="3" />
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209 <param name="dimr" value="true" />
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210 <param name="mode" value="pca" />
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211 <param name="logscale" value="true" />
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212 </conditional>
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213 </expand>
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214 </section>
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215 <section name="clust" >
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216 <param name="metric" value="euclidean" />
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217 <param name="funcluster" value="hclust" />
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218 <expand macro="test_nondef" >
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219 <param name="fselect" value="false" />
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220 <param name="knn" value="5" />
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221 <param name="sat" value="false" />
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222 <param name="samp" value="10" />
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223 <param name="cln" value="10" />
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224 <param name="clustnr" value="10" />
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225 <param name="bootnr" value="30" />
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226 <param name="rseed" value="17000" />
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227 </expand>
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228 </section>
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229 <section name="outlier" >
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230 <param name="outminc" value="3" />
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231 <param name="outlg" value="5" />
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232 <param name="final" value="true" />
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233 <expand macro="test_nondef" >
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234 <param name="probthr" value="0.01" />
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235 <param name="outdistquant" value="0.5" />
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236 <param name="rfseed" value="12345" />
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237 <param name="nbfactor" value="5" />
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238 <param name="nbtree" value="10" />
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239 </expand>
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240 </section>
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241 <section name="tsne" >
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242 <param name="perplexity" value="20" />
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243 <param name="knn" value="6" />
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244 <expand macro="test_nondef" >
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245 <param name="initial_cmd" value="false" />
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246 <param name="rseed_tsne" value="15555" />
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247 <param name="rfseed_fr" value="15555" />
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248 </expand>
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249 </section>
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250 </conditional>
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251 <output name="outgenelist" value="intestinal_advanced.genelist" />
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252 <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
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253 </test>
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254 </macro>
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255 <token name="@FILTNORM_CHEETAH@"><![CDATA[
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256 ## Perform do.filter
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257 use.filtnormconf = TRUE
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258
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259 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
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260 use.cluster = FALSE
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iuc
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261
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262 in.table = read.table(
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263 '${intable}',
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264 stringsAsFactors = F,
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265 na.strings=c("NA", "-", "?", "."),
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iuc
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266 sep='\t',
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267 header=TRUE,
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268 row.names=1
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iuc
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269 )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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270
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271 ## Hidden flag to use test data instead
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272 ## see: test-data/use.intestinal
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iuc
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273
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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274 use.test.data = (names(in.table)[1] == "test")
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275
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276 sc = NULL
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277 if (use.test.data) {
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278 sc = SCseq(intestinalData)
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279 message("Loading test data from library")
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280 } else {
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281 sc = SCseq(in.table)
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282 }
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283
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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284
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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285 filt = formals(filterdata)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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286 filt.ccc = formals(CCcorrect)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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287 filt.use.ccorrect = FALSE
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iuc
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288 filt.lbatch.regexes = NULL
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iuc
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289
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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290 filt\$mintotal = as.integer( '$filt.mintotal' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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291 filt\$minexpr = as.integer( '$filt.minexpr' )
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iuc
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292 filt\$minnumber = as.integer( '$filt.minnumber' )
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293 #if str($filt.use.def) == "no":
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294 filt\$knn = as.integer( '$filt.use.knn' )
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295 filt\$ccor = as.numeric( '$filt.use.ccor' )
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296 filt\$bmode = as.character( '$filt.use.bmode' )
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297 #if $filt.use.LBatch_regexes:
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iuc
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298 filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
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299 #end if
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300 #if $filt.use.CGenes:
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301 filt\$CGenes = string2textvector( '$filt.use.CGenes' )
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302 #end if
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303 #if $filt.use.FGenes:
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304 filt\$FGenes = string2textvector( '$filt.use.FGenes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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305 #end if
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306 #if str($filt.use.ccc.use) == "yes"
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307 filt.use.ccorrect = TRUE
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308 #if $filt.use.ccc.vset:
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iuc
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309 filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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310 #end if
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311 #if $filt.use.ccc.ncomp:
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312 filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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313 #end if
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314 filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
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315 filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
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316 filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
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317 filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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318 filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
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319 #end if
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320 #end if
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321
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322 out.pdf = '${outpdf}'
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323 out.rdat = '${outrdat}'
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324
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iuc
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diff changeset
325 ]]></token>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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326 <token name="@CLUSTER_CHEETAH@"><![CDATA[
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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327
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iuc
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328 in.rdat = readRDS('${inputrds}')
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iuc
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329
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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diff changeset
330 sc = in.rdat
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331
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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332 ## Perform do.filter
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333 use.filtnormconf = FALSE
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334
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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335 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
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336 use.cluster = TRUE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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337
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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338
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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339 clust.compdist = formals(compdist)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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340 clust.clustexp = formals(clustexp)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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341 clust.compdist\$metric = as.character( '$clust.metric' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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342 clust.clustexp\$FUNcluster = as.character( '$clust.funcluster' )
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iuc
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343
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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344 #if str($clust.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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345
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346 clust.compdist\$FSelect = as.logical( '$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 $clust.use.knn:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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348 clust.compdist\$knn = as.integer( '$clust.use.knn' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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349 #end if
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iuc
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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
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351 #if $clust.use.samp:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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352 clust.clustexp\$samp = as.integer( '$clust.use.samp' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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353 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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354 #if $clust.use.cln:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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355 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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356 clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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357 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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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
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359 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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360 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
361
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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362 outlier.use.randomforest = FALSE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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363 outlier.findoutliers = formals(findoutliers)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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364 outlier.clustheatmap = formals(clustheatmap)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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365 outlier.rfcorrect = formals(rfcorrect)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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366
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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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
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368 outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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369 outlier.rfcorrect\$final = as.logical( '$outlier.final' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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370
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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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
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372 #if $outlier.use.nbtree:
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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373 outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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374 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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375 outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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376 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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377 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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378 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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379 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
380
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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381 cluster.comptsne = formals(comptsne)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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382 cluster.compfr = formals(compfr)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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383
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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384 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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385 cluster.compfr\$knn = as.integer( '$tsne.knn' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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386 #if str($tsne.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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387 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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388 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
389 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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390 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
391
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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392 genelist.tablelim = as.integer( '$extra.tablelim' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
393 genelist.plotlim = as.integer( '$extra.plotlim' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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394 genelist.foldchange = as.integer( '$extra.foldchange' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
395 genelist.pvalue = as.numeric( '$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
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397 out.pdf = '${outpdf}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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398 out.rdat = '${outrdat}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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399 out.genelist = '${outgenelist}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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parents:
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400
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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401 ]]>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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402 </token>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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403 </macros>