annotate raceid_inspectclusters.xml @ 8:2b0d3e2f402a draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author iuc
date Mon, 20 Dec 2021 10:13:54 +0000
parents be4646256624
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1 <tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>examines gene expression within clusters</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_cheetah.xml</import>
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6 <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
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7 <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" >
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8 <param name="name_set" type="text" optional="true" label="Name of Set" >
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9 <!-- Aname, Bname -->
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10 <expand macro="sanitize_title" />
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11 </param>
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12 <conditional name="meth" >
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13 <param name="type" type="select" label="Selection method" >
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14 <option value="cln" selected="true">Cluster Numbers</option>
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15 <option value="regex" >Regular Expression</option>
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16 <option value="manual" >Manual Selection</option>
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17 </param>
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18 <when value="cln" >
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19 <param name="selector" type="text" value="" label="List of clusters" help="Clusters should be listed delimited by commas (e.g. 3,4,5)" >
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20 <expand macro="sanitize_numeric_vector" />
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21 </param>
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22 </when>
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23 <when value="regex" >
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24 <param name="selector" type="text" value="" label="Regular Expression to select gene names" >
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25 <expand macro="sanitize_regex" />
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26 </param>
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27 </when>
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28 <when value="manual" >
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29 <param name="selector" type="text" value="" label="List of genes" >
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30 <expand macro="sanitize_string_vector" />
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31 </param>
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32 </when>
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33 </conditional>
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34 </section>
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35 </macro>
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36 </macros>
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37 <expand macro="requirements" />
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38 <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&#38;&#62; '$outlog'" />
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39 <inputs>
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40 <param name="inputrds" type="data" format="rds" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" />
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41 <conditional name="plotgen">
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42 <param name="do_opt" type="select" label="Plot Clusters?" help="Generates tSNE and F-R plots" >
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43 <option value="yes" selected="true" >Yes</option>
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44 <option value="no" >No</option>
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45 </param>
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46 <when value="no" />
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47 <when value="yes" >
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48 <param name="clusts_plot" type="text" label="Cluster Numbers to plot" value="" help="Leave blank to plot all clusters" optional="true" >
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49 <expand macro="sanitize_numeric_vector" />
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50 </param>
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51 </when>
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52 </conditional>
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53 <conditional name="plotsym" >
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54 <param name="do_opt" type="select" label="Perform Subset Analysis?" >
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55 <expand macro="yesno_checkedno" />
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56 </param>
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57 <when value="no" />
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58 <when value="yes">
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59 <param name="types_regex" type="text" optional="true" label="Types Regex (removal)" help="Regular expression to be used to remove portions of the cell names, in order to indicate cell type. e.g. if your cells are labelled as 'cdk5_1, cdk5_2, glow_1, glow_2', then a regex of '_\\d$' would trim off the ends and set the cell types to 'cdk5, cdk5, glow, glow'. " >
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60 <expand macro="sanitize_regex" />
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61 </param>
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62 <expand macro="use_defaults_no" >
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63 <param name="subset_regex" type="text" optional="true" label="Subset of Types: Regex (select)" help="Regular expression to be used to select for cell types of interest. e.g. if we are only interested in 'cdk5' positive cells, then we would simply put 'cdk5' here. ">
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64 <expand macro="sanitize_regex" />
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65 </param>
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66 <param name="fr" type="boolean" checked="false" label="Output FR map instead of tSNE" help="Performs a Fruchterman-Rheingold projection instead of tSNE" />
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67 </expand>
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68 </when>
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69 </conditional>
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70 <conditional name="gois" >
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71 <param name="do_opt" type="select" label="Examine Genes of Interest" >
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72 <expand macro="yesno_checkedno" />
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73 </param>
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74 <when value="no" />
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75 <when value="yes">
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76 <param name="inspect_goi_genes" type="text" value="" label="Genes to Examine" >
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77 <expand macro="sanitize_string_vector" />
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78 </param>
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79 <param name="inspect_goi_cells" type="text" optional="true" label="Cells to Examine" help="Leave blank to examine all" ><!-- "":NULL -->
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80 <expand macro="sanitize_string_vector" />
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81 </param>
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82 <expand macro="use_defaults_no" >
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83 <!-- Yes, examine genes of interest, but no do not use defaults... -->
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84 <param name="inspect_goi_imputed" type="boolean" checked="false" label="Impute Genes" help="Only works if k-nearest neighbours was used in the clustering" />
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85 <param name="plotexp_n" type="text" optional="true" label="Title of plot" help="If blank, the list of genes are used" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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86 <expand macro="sanitize_title" />
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87 </param>
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88 <param name="plotmarkg_cthr" type="integer" min="0" value="0" label="Cluster Threshold" help="Include only clusters with cells greater than this" />
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89 <param name="plotmarkg_cl" type="text" optional="true" label="Cluster List" help="List of cluster numbers to include. Leave blank to include all" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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90 <expand macro="sanitize_numeric_vector" />
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91 </param><!-- "":NULL -->
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92 <param name="plotmarkg_order_cells" type="boolean" checked="false" label="Order Cells" help="Order heatmap by cell names, not by cluster" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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93 <param name="plotmarkg_aggr" type="boolean" checked="false" label="Average Expression" help="Show only average expression for each cluster" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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94 <param name="plotmarkg_norm" type="boolean" checked="false" label="Normalise Gene Expression " help="Normalise gene expression to 1 to depict genes on the same scale" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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95 <param name="plotmarkg_flo" type="integer" max="-5" optional="true" label="Lower-bound for Gene Expression" /><!-- negative or null vals only for this seem to work-->
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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96 <param name="plotmarkg_cap" type="integer" min="1" optional="true" label="Upper-bound for Gene Expression" />
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97 <param name="plotmarkg_samples" type="text" optional="true" label="Regex to Select Sample Names For Each cell" >
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98 <expand macro="sanitize_regex" />
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99 </param>
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100 <param name="plotmarkg_cluster_cols" type="boolean" checked="false" label="Cluster columns" />
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101 <param name="plotmarkg_cluster_rows" type="boolean" checked="true" label="Cluster rows" />
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102 <param name="plotmarkg_cluster_set" type="boolean" checked="false" label="Order Clusters by Heirarchal Clustering of Cluster Medoids." />
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103 </expand>
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104 </when>
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105 </conditional>
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106 <conditional name="diffgtest" >
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107 <param name="do_opt" type="select" label="Differential Gene Testing" >
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parents: 0
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108 <expand macro="yesno_checkedno" />
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109 </param>
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110 <when value="no" />
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parents: 0
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111 <when value="yes" >
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112 <expand macro="select_cells" sectionname="set_a" sectiontitle="Cells in Set A" />
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113 <expand macro="select_cells" sectionname="set_b" sectiontitle="Cells in Set B" />
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114 <expand macro="use_defaults_no" >
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115 <param name="plotdiffg_pthr" type="float" min="0" max="1" value="0.05" label="P-value cutoff" help="Cutoff for displaying differentially expressed genes" />
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116 <param name="plotdiffg_padj" type="boolean" checked="true" label="Apply B-H Correction" help="Display genes with a Benjamini-Hochberg corrected false discovery rate lower than the above P-value threshold" />
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117 <param name="plotdiffg_lthr" type="float" min="0" value="0" label="Log2-Fold Threshold" help="Differentially expressed genes are displayed only for log2 fold-changes higher than this" />
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118 <param name="plotdiffg_mthr" type="float" optional="true" label="Log2 Mean Threshold" help="Differentially expressed genes are displayed only for log2 mean expression greater than this" /><!-- opt:-Inf -->
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119 <param name="plotdiffg_show_names" type="boolean" checked="false" label="Display Gene Names" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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120 </expand>
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121 </when>
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122 </conditional>
0
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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123 </inputs>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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124 <outputs>
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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125 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents: 0
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126 <data name="outlog" format="txt" hidden="true" /><!-- useful for debugging, but hide from user -->
0
9fec5dd8fbb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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127 </outputs>
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128 <tests>
4
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129 <test><!-- general plots, plotgen -->
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130 <param name="inputrds" value="out_cluster_default.rdat" />
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parents: 0
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131 <conditional name="plotgen" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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132 <param name="do_opt" value="yes" />
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iuc
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133 </conditional>
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iuc
parents: 0
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134 <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" />
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135 </test>
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iuc
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136 <test><!-- general plots, plotgen with cluster 1,8,5 only -->
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents: 0
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137 <param name="inputrds" value="out_cluster_default.rdat" />
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iuc
parents: 0
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138 <conditional name="plotgen" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
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139 <param name="do_opt" value="yes" />
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parents: 0
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140 <param name="clusts_plot" value="1,8,5" />
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141 </conditional>
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142 <output name="outpdf" value="out_cluster_general_default.pdf" lines_diff="30" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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143 </test>
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144 <test><!-- default test, plotsym -->
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145 <param name="inputrds" value="out_cluster_default.rdat" />
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parents: 0
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146 <conditional name="plotsym" >
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parents: 0
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147 <param name="do_opt" value="yes" />
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148 <param name="types_regex" value="\\_\\d+" />
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parents: 0
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149 <expand macro="test_nondef" >
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150 <param name="subset_regex" value="IV|V" />
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151 </expand>
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152 </conditional>
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153 <conditional name="gois" >
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parents: 0
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154 <param name="do_opt" value="yes" />
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parents: 0
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155 <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" />
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156 </conditional>
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157 <output name="outpdf" value="out_cluster_inspect_default.pdf" lines_diff="30" />
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158 </test>
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159 <test><!-- Advanced 1 -->
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160 <param name="inputrds" value="out_cluster_default.rdat" />
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iuc
parents: 0
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161 <conditional name="plotsym" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
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162 <param name="do_opt" value="yes" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
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163 <param name="types_regex" value="\\_\\d+" />
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iuc
parents: 0
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164 <expand macro="test_nondef" >
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parents: 0
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165 <param name="subset_regex" value="IV|V" />
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166 <param name="fr" value="true" />
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diff changeset
167 </expand>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
168 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
169 <conditional name="gois" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
170 <param name="do_opt" value="yes" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
171 <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
172 <expand macro="test_nondef" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
173 <param name="inspect_goi_imputed" value="false" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
174 <param name="plotexp_n" value="Test Title" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
175 <param name="plotmarkg_order_cells" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
176 <param name="plotmarkg_aggr" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
177 <param name="plotmarkg_norm" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
178 <param name="plotmarkg_flo" value="-10" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
179 <param name="plotmarkg_cap" value="100" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
180 <param name="plotmarkg_samples" value="(\\_\\d+)$" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
181 <param name="plotmarkg_cluster_cols" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
182 <param name="plotmarkg_cluster_rows" value="false" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
183 <param name="plotmarkg_cluster_set" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
184 </expand>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
185 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
186 <conditional name="diffgtest" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
187 <param name="do_opt" value="yes" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
188 <section name="set_a" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
189 <param name="name_set" value="Test set A" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
190 <conditional name="meth" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
191 <param name="type" value="regex" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
192 <param name="selector" value="^V5.*" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
193 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
194 </section>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
195 <section name="set_b" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
196 <param name="name_set" value="Test set B" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
197 <conditional name="meth" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
198 <param name="type" value="manual" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
199 <param name="selector" value="I5d_3,I5d_4,I5d_6,I5d_8,I5d_9,I5d_10,I5d_11,I5d_12,I5d_13,I5d_14" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
200 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
201 </section>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
202 <expand macro="test_nondef" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
203 <param name="plotdiffg_pthr" value="0.1" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
204 <param name="plotdiffg_padj" value="false" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
205 <param name="plotdiffg_lthr" value="0.2" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
206 <param name="plotdiffg_mthr" value="0.2" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
207 <param name="plotdiffg_show_names" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
208 </expand>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
209 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
210 <output name="outpdf" value="out_cluster_inspect_advanced1.pdf" lines_diff="30"/>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
211 </test>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
212 <test><!-- Advanced 2 -->
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
213 <param name="inputrds" value="out_cluster_default.rdat" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
214 <conditional name="plotsym" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
215 <param name="do_opt" value="yes" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
216 <expand macro="test_nondef" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
217 <param name="fr" value="false" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
218 </expand>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
219 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
220 <conditional name="gois" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
221 <param name="do_opt" value="yes" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
222 <param name="inspect_goi_genes" value="Sp1,Spc24,Spcs1,Spcs2,Spcs3" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
223 <expand macro="test_nondef" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
224 <param name="plotexp_n" value="Test Title 2" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
225 <param name="plotmarkg_order_cells" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
226 <param name="plotmarkg_aggr" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
227 <param name="plotmarkg_norm" value="false" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
228 <param name="plotmarkg_flo" value="-10" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
229 <param name="plotmarkg_cap" value="10" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
230 <param name="plotmarkg_cluster_cols" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
231 <param name="plotmarkg_cluster_rows" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
232 <param name="plotmarkg_cluster_set" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
233 </expand>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
234 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
235 <conditional name="diffgtest" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
236 <param name="do_opt" value="yes" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
237 <section name="set_a" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
238 <param name="name_set" value="Test set A" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
239 <conditional name="meth" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
240 <param name="type" value="regex" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
241 <param name="selector" value="^IV.*" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
242 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
243 </section>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
244 <section name="set_b" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
245 <param name="name_set" value="Test set B" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
246 <conditional name="meth" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
247 <param name="type" value="cln" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
248 <param name="selector" value="3" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
249 </conditional>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
250 </section>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
251 <expand macro="test_nondef" >
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
252 <param name="plotdiffg_pthr" value="0.8" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
253 <param name="plotdiffg_padj" value="true" />
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents: 0
diff changeset
254 <param name="plotdiffg_lthr" value="0.8" />
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255 <param name="plotdiffg_mthr" value="0.8" />
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256 <param name="plotdiffg_show_names" value="false" />
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257 </expand>
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258 </conditional>
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259 <output name="outpdf" value="out_cluster_inspect_advanced2.pdf" lines_diff="30"/>
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260 </test>
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261 <test><!-- Advanced 3 -->
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262 <param name="inputrds" value="out_cluster_default.rdat" />
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263 <conditional name="plotsym" >
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264 <param name="do_opt" value="no" />
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265 </conditional>
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266 <conditional name="gois" >
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267 <param name="do_opt" value="no" />
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268 </conditional>
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269 <conditional name="diffgtest" >
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270 <param name="do_opt" value="yes" />
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271 <section name="set_a" >
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272 <param name="name_set" value="Test set A" />
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273 <conditional name="meth" >
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274 <param name="type" value="cln" />
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275 <param name="selector" value="1,2" />
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276 </conditional>
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277 </section>
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278 <section name="set_b" >
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279 <param name="name_set" value="Test set B" />
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280 <conditional name="meth" >
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281 <param name="type" value="cln" />
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282 <param name="selector" value="3,4,6" />
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283 </conditional>
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284 </section>
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285 </conditional>
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286 <output name="outpdf" value="out_diffgene_multiple.pdf" lines_diff="30"/>
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287 </test>
0
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288 </tests>
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289 <help><![CDATA[
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290
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291 RaceID3
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292 =========
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293
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294 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.
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295
8
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296 This module inspects the clusters generated from the previous clustering step (and requires the output RDS file from it as input).
0
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297
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298 The tool offers three modes of inspection which can all be activated at the same time, resulting in a single PDF report:
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299
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300 * Plot All Clusters:
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301 * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots.
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302 * Perform Subset Analysis:
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303 * tSNE and F-R plots with cells whose name match the specified regex highlighted
4
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304
0
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305 * Examine Genes of Interest:
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306 * Expression plots highlighting a gene or genes of interest across all clusters
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307
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308 * Differential Gene Testing:
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309 * Examining the expression between
0
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310
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311 * A list of the most differentially expressed genes in each cluster
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312 * An output PDF that provides heatmaps for:
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313 * The initial and final clustering (as determined using random forest)
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314 * Heatmaps for each of the most differentially expressed genes in each cluster
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315
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316 The tool requires the RDS input from the previous filtering / normalisation / confounder removal step to work.
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317
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318
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319
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320 ]]></help>
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321 <expand macro="citations" />
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322 </tool>