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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:47 -0400
parents 78fcfc04fcfe
children
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1 <?xml version="1.0"?>
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2 <tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy1">
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3 <description>visualize Cuffdiff output</description>
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4 <macros>
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5 <import>cummeRbund_macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
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9 <requirement type="package" version="1.0.4">r-argparse</requirement>
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10 <requirement type="package" version="3.4.1">r-base</requirement>
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11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>
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12 </requirements>
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13 <code file="cummeRbund_options.py"/>
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14 <command detect_errors="aggressive">
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15 <![CDATA[
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16 #for i, p in enumerate($plots):
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17 Rscript --vanilla --slave '$__tool_directory__/cummeRbund.R'
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18 --input '$input_database' --width $p.width --height $p.height --type "${p.plot.type}"
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19 --outfile 'plot-${p.plot.type}-${i}.png'
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20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
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21 $p.plot.replicates
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22 #elif $p.plot.type == "scatter":
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23 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
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24 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
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25 --features $p.plot.multiple_genes.features --gene_selector
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26 #for gene in $p.plot.multiple_genes.genes:
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27 --genes '$gene.gene_id'
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28 #end for
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29 #end if
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30 #elif $p.plot.type == "maplot":
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31 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
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32 #elif $p.plot.type == "volcano":
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33 --x "$p.plot.x" --y "$p.plot.y"
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34 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
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35 --features $p.plot.multiple_genes.features --gene_selector
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36 #for gene in $p.plot.multiple_genes.genes:
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37 --genes '$gene.gene_id'
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38 #end for
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39 #end if
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40 #elif $p.plot.type == "heatmap":
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41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
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42 #if len($p.plot.genes) > 0:
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43 --gene_selector
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44 #for gene in $p.plot.genes:
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45 --genes '$gene.gene_id'
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46 #end for
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47 #end if
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48 #elif $p.plot.type == "cluster":
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49 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
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50 #if len($p.plot.genes) > 0:
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51 #for gene in $p.plot.genes:
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52 --genes '$gene.gene_id'
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53 #end for
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54 #end if
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55 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
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56 #if $p.plot.type == "expressionplot":
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57 $p.plot.draw_summary
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58 #end if
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59 --features $p.plot.features $p.plot.error_bars --genes '$p.plot.gene_id' $p.plot.replicates $p.plot.log10
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60 #end if
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61 #if $p.plot.type == "density":
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62 $p.plot.log10
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63 #end if
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64 > '${output}' 2>&1 ;
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65 #end for
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66 ]]></command>
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67 <inputs>
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68 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
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69 <repeat name="plots" title="Plots">
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70 <param name="width" type="integer" value="1280" label="The width of the image"/>
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71 <param name="height" type="integer" value="960" label="The height of the image"/>
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72 <conditional name="plot">
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73 <param name="type" type="select" label="Plot type">
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74 <option value="density" selected="true">Density</option>
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75 <option value="boxplot">Boxplot</option>
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76 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
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77 <option value="pca">Principal Component Analysis (PCA) Plot</option>
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78 <option value="dendrogram">Dendrogram</option>
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79 <option value="scatter">Scatter</option>
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80 <option value="volcano">Volcano</option>
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81 <option value="heatmap">Heatmap</option>
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82 <option value="dispersion">Dispersion</option>
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83 <option value="fpkmSCV">Squared Coefficient of Variation</option>
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84 <option value="scatterMatrix">Scatter Matrix</option>
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85 <option value="cluster">Cluster</option>
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86 <option value="expressionplot">Expression Plot</option>
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87 <option value="expressionbarplot">Expression Bar Plot</option>
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88 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
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89 </param>
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90 <when value="density">
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91 <expand macro="replicates_checkbox" />
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92 <expand macro="log10_checkbox" />
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93 </when>
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94 <when value="mds">
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95 <expand macro="replicates_checkbox" />
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96 </when>
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97 <when value="pca">
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98 <expand macro="replicates_checkbox" />
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99 </when>
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100 <when value="boxplot">
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101 <expand macro="replicates_checkbox" />
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102 <expand macro="log10_checkbox" />
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103 </when>
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104 <when value="dendrogram">
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105 <expand macro="replicates_checkbox" />
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106 </when>
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107 <when value="scatter">
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108 <expand macro="xy_selector" />
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109 <expand macro="log10_checkbox" />
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110 <param name="smooth" type="boolean" truevalue="--smooth" falsevalue="" checked="True" label="Add a smooth-fit regression line"/>
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111 <expand macro="multiple_genes_conditional" />
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112 </when>
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113 <when value="volcano">
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114 <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
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115 <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
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116 <expand macro="multiple_genes_conditional" />
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117 </when>
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118 <when value="heatmap">
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119 <expand macro="features_selector" />
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120 <expand macro="genes_selector" />
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121 <param name="clustering" type="select" label="Cluster by">
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122 <option value="row">Row</option>
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123 <option value="column">Column</option>
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124 <option value="both" selected="true">Both</option>
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125 <option value="none">None</option>
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126 </param>
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127 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
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128 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display row labels?"/>
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129 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
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130 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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131 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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132 <when value="cluster">
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133 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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134 <expand macro="genes_selector" />
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135 <param name="k" type="integer" value="1" label="Number of pre-defined clusters to attempt to find."/>
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136 <param name="iter_max" type="integer" value="100" label="Max iterations"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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137 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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138 <when value="maplot">
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139 <expand macro="xy_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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140 <param name="count" type="boolean" truevalue="--count" falsevalue="" checked="False" label="Use Count?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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141 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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142 <when value="dispersion" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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143 <when value="fpkmSCV" />
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144 <when value="scatterMatrix" />
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145 <when value="expressionplot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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146 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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147 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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148 <param name="draw_summary" type="boolean" truevalue="--summary" falsevalue="" checked="False" label="Draw a 'summary' line with mean FPKM values for each condition?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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149 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
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150 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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151 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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152 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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153 <when value="expressionbarplot">
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154 <expand macro="features_selector" />
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155 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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156 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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157 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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158 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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159 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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160 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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161 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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162 </inputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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163 <outputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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164 <data format="txt" name="output" label="${tool.name} on ${on_string}">
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165 <discover_datasets pattern="plot-(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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166 </data>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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167 </outputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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168 <tests>
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169 <test>
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170 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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171 <repeat name="plots">
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172 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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173 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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174 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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175 <param name="type" value="maplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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176 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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177 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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178 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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179 </repeat>
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180 <output name="output" ftype="txt">
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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181 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0
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182 <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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183 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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184 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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185 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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186 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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187 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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188 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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189 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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190 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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191 <param name="type" value="scatter" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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192 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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193 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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194 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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195 </repeat>
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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196 <output name="output" ftype="txt">
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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197 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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198 <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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199 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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200 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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201 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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202 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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203 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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204 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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205 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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206 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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207 <param name="type" value="dispersion" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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208 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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209 </repeat>
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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210 <output name="output" ftype="txt">
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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211 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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212 <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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213 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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214 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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215 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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216 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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217 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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218 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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219 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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220 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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221 <param name="type" value="scatterMatrix" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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222 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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223 </repeat>
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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224 <output name="output" ftype="txt">
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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225 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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226 <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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227 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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228 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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229 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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230 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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231 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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232 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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233 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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234 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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235 <param name="type" value="pca" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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236 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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237 </repeat>
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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238 <output name="output" ftype="txt">
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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239 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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240 <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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241 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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242 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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243 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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244 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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245 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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246 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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247 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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248 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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249 <param name="type" value="expressionplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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250 <param name="features" value="gene" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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251 <param name="gene_id" value="XLOC_000059" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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252 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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253 </repeat>
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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254 <output name="output" ftype="txt">
c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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255 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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256 <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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257 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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258 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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259 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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260 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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261 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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262 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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263 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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264 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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265 <param name="features" value="gene" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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266 <param name="type" value="expressionbarplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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267 <param name="gene_id" value="XLOC_000039" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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268 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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269 </repeat>
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c3b54a4b7741 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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270 <output name="output" ftype="txt">
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271 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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272 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
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273 </output>
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274 </test>
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275 <test>
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276 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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277 <repeat name="plots">
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278 <param name="width" value="1280" />
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279 <param name="height" value="960" />
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280 <conditional name="plot">
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281 <param name="type" value="heatmap" />
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282 <repeat name="genes">
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283 <param name="gene_id" value="XLOC_000030" />
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284 </repeat>
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285 <repeat name="genes">
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286 <param name="gene_id" value="XLOC_000037" />
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287 </repeat>
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288 </conditional>
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289 </repeat>
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290 <output name="output" ftype="txt">
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291 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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292 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
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293 </output>
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294 </test>
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295 <test>
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296 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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297 <repeat name="plots">
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298 <param name="width" value="1280" />
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299 <param name="height" value="960" />
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300 <conditional name="plot">
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301 <param name="type" value="density" />
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302 </conditional>
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303 </repeat>
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304 <output name="output" ftype="txt">
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305 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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306 <discovered_dataset designation="density-0" ftype="png" file="density.png" />
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307 </output>
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308 </test>
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309 <test>
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310 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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311 <repeat name="plots">
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312 <param name="width" value="1280" />
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313 <param name="height" value="960" />
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314 <conditional name="plot">
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315 <param name="type" value="dendrogram" />
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316 </conditional>
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317 </repeat>
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318 <output name="output" ftype="txt">
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319 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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320 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
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321 </output>
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322 </test>
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323 <test>
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324 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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325 <repeat name="plots">
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326 <param name="width" value="1280" />
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327 <param name="height" value="960" />
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328 <conditional name="plot">
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329 <param name="type" value="volcano" />
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330 <param name="x" value="q1" />
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331 <param name="y" value="q2" />
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332 </conditional>
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333 </repeat>
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334 <output name="output" ftype="txt">
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335 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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336 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
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337 </output>
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338 </test>
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339 <test>
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340 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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341 <repeat name="plots">
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342 <param name="width" value="1280" />
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343 <param name="height" value="960" />
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344 <conditional name="plot">
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345 <param name="type" value="boxplot" />
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346 </conditional>
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347 </repeat>
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348 <output name="output" ftype="txt">
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349 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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350 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
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351 </output>
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352 </test>
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353 <test>
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354 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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355 <repeat name="plots">
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356 <param name="width" value="1280" />
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357 <param name="height" value="960" />
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358 <conditional name="plot">
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359 <param name="type" value="fpkmSCV" />
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360 </conditional>
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361 </repeat>
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362 <output name="output" ftype="txt">
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363 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
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364 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
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365 </output>
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366 </test>
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367 </tests>
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368 <help><![CDATA[
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369 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
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370
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371 ------
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372
5
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373 Based on the `cummeRbund wrapper <https://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
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374 ]]></help>
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375 <citations>
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376 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
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377 </citations>
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378 </tool>