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annotate cummeRbund.xml @ 4:ba8fde59843d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:18:39 -0400
parents 3a0ade59306a
children 78fcfc04fcfe
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1 <?xml version="1.0"?>
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ba8fde59843d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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2 <tool id="cummeRbund" name="cummeRbund" version="1.0.1">
ba8fde59843d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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3 <description>visualize Cuffdiff output</description>
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4 <requirements>
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5 <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="package" version="2.8.2">cummeRbund</requirement>
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8 </requirements>
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9 <expand macro="stdio" />
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10 <macros>
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11 <import>cummeRbund_macros.xml</import>
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12 </macros>
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13 <code file="cummeRbund_options.py"/>
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14 <command>
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15 <![CDATA[
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16 #for i, p in enumerate($plots):
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17 R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args
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18 --input "${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 #for gene in $p.plot.genes:
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44 --genes ${gene.gene_id}
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45 #end for
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46 #end if
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47 #elif $p.plot.type == "cluster":
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48 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
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49 #if len($p.plot.genes) > 0:
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50 #for gene in $p.plot.genes:
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51 --genes ${gene.gene_id}
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52 #end for
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53 #end if
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54 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
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55 #if $p.plot.type == "expressionplot":
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56 $p.plot.draw_summary
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57 #end if
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58 --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10
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59 #end if
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60 #if $p.plot.type == "density":
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61 $p.plot.log10
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62 #end if
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63 > "${output}" 2>&1 ;
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64 #end for
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65 ]]></command>
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66 <inputs>
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67 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
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68 <repeat name="plots" title="Plots">
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69 <param name="width" type="integer" value="1280" label="The width of the image"/>
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70 <param name="height" type="integer" value="960" label="The height of the image"/>
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71 <conditional name="plot">
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72 <param name="type" type="select" label="Plot type">
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73 <option value="density" selected="true">Density</option>
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74 <option value="boxplot">Boxplot</option>
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75 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
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76 <option value="pca">Principal Component Analysis (PCA) Plot</option>
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77 <option value="dendrogram">Dendrogram</option>
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78 <option value="scatter">Scatter</option>
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79 <option value="volcano">Volcano</option>
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80 <option value="heatmap">Heatmap</option>
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81 <option value="dispersion">Dispersion</option>
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82 <option value="fpkmSCV">Squared Coefficient of Variation</option>
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83 <option value="scatterMatrix">Scatter Matrix</option>
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84 <option value="cluster">Cluster</option>
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85 <option value="expressionplot">Expression Plot</option>
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86 <option value="expressionbarplot">Expression Bar Plot</option>
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87 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
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88 </param>
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89 <when value="density">
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90 <expand macro="replicates_checkbox" />
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91 <expand macro="log10_checkbox" />
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92 </when>
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93 <when value="mds">
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94 <expand macro="replicates_checkbox" />
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95 </when>
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96 <when value="pca">
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97 <expand macro="replicates_checkbox" />
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98 </when>
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99 <when value="boxplot">
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100 <expand macro="replicates_checkbox" />
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101 <expand macro="log10_checkbox" />
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102 </when>
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103 <when value="dendrogram">
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104 <expand macro="replicates_checkbox" />
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105 </when>
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106 <when value="scatter">
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107 <expand macro="xy_selector" />
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108 <expand macro="log10_checkbox" />
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109 <param name="smooth" type="boolean" truevalue="--smooth" falsevalue="" checked="True" label="Add a smooth-fit regression line"/>
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110 <expand macro="multiple_genes_conditional" />
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111 </when>
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112 <when value="volcano">
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113 <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
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114 <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
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115 <expand macro="multiple_genes_conditional" />
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116 </when>
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117 <when value="heatmap">
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118 <expand macro="features_selector" />
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119 <expand macro="genes_selector" />
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120 <param name="clustering" type="select" label="Cluster by">
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121 <option value="row">Row</option>
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122 <option value="column">Column</option>
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123 <option value="both" selected="true">Both</option>
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124 <option value="none">None</option>
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125 </param>
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126 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
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127 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/>
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128 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
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129 <expand macro="log10_checkbox" />
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130 </when>
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131 <when value="cluster">
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132 <expand macro="features_selector" />
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133 <expand macro="genes_selector" />
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134 <param name="k" type="integer" value="1" label="Number of pre-defined clusters to attempt to find."/>
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135 <param name="iter_max" type="integer" value="100" label="Max iterations"/>
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136 </when>
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137 <when value="maplot">
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138 <expand macro="xy_selector" />
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139 <param name="count" type="boolean" truevalue="--count" falsevalue="" checked="False" label="Use Count?"/>
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140 </when>
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141 <when value="dispersion" />
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142 <when value="fpkmSCV" />
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143 <when value="scatterMatrix" />
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144 <when value="expressionplot">
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145 <expand macro="features_selector" />
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146 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
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147 <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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148 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
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149 <expand macro="replicates_checkbox" />
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150 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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151 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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152 <when value="expressionbarplot">
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153 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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154 <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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155 <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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156 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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157 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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158 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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159 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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160 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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161 </inputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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162 <outputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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163 <data format="txt" name="output" label="${tool.name} on ${on_string}">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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164 <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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165 </data>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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166 </outputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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167 <tests>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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168 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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169 <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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170 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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171 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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172 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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173 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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174 <param name="type" value="maplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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175 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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176 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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177 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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178 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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179 <output name="output" ftype="txt" file="maplot.txt" lines_diff="2">
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180 <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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181 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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182 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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183 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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184 <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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185 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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186 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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187 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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188 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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189 <param name="type" value="scatter" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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190 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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191 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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192 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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193 </repeat>
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194 <output name="output" ftype="txt" file="scatter.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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195 <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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196 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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197 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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198 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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199 <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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200 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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201 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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202 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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203 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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204 <param name="type" value="dispersion" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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205 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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206 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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207 <output name="output" ftype="txt" file="dispersion.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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208 <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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209 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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210 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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211 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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212 <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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213 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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214 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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215 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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216 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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217 <param name="type" value="scatterMatrix" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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218 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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219 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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220 <output name="output" ftype="txt" file="scatterMatrix.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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221 <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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222 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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223 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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224 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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225 <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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226 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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227 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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228 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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229 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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230 <param name="type" value="pca" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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231 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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232 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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233 <output name="output" ftype="txt" file="pca.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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234 <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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235 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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236 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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237 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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238 <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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239 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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240 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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241 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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242 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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243 <param name="type" value="expressionplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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244 <param name="features" value="gene" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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245 <param name="gene_id" value="XLOC_000059" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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246 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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247 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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248 <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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249 <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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250 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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251 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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252 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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253 <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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254 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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255 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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256 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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257 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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258 <param name="features" value="gene" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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259 <param name="type" value="expressionbarplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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260 <param name="gene_id" value="XLOC_000039" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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261 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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262 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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263 <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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264 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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265 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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266 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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267 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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268 <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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269 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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270 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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271 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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272 <conditional name="plot">
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273 <param name="type" value="heatmap" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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274 <repeat name="genes">
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275 <param name="gene_id" value="XLOC_000078" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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276 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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277 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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278 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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279 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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280 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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281 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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282 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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283 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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284 <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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285 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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286 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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287 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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288 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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289 <param name="type" value="density" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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290 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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291 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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292 <output name="output" ftype="txt" file="density.txt" lines_diff="2">
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293 <discovered_dataset designation="density-0" ftype="png" file="density.png" />
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294 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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295 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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296 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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297 <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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298 <repeat name="plots">
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299 <param name="width" value="1280" />
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300 <param name="height" value="960" />
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301 <conditional name="plot">
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302 <param name="type" value="dendrogram" />
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303 </conditional>
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304 </repeat>
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305 <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">
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306 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.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="volcano" />
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316 <param name="x" value="q1" />
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317 <param name="y" value="q2" />
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318 </conditional>
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319 </repeat>
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320 <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">
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321 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
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322 </output>
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323 </test>
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324 <test>
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325 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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326 <repeat name="plots">
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327 <param name="width" value="1280" />
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328 <param name="height" value="960" />
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329 <conditional name="plot">
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330 <param name="type" value="boxplot" />
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331 </conditional>
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332 </repeat>
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333 <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">
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334 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
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335 </output>
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336 </test>
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337 <test>
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338 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
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339 <repeat name="plots">
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340 <param name="width" value="1280" />
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341 <param name="height" value="960" />
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342 <conditional name="plot">
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343 <param name="type" value="fpkmSCV" />
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344 </conditional>
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345 </repeat>
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346 <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">
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347 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
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348 </output>
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349 </test>
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350 </tests>
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351 <help><![CDATA[
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352 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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353
0
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354 ------
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355
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356 Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
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357 ]]></help>
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358 <citations>
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359 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
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360 </citations>
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361 </tool>