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1 <tool id="cummerbund" name="cummeRbund" version="0.0.6">
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2
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3 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
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4
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5 <command interpreter="python">
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6 cummerbund_wrapper.py
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7 --r-script ${script_file}
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8 --html-report-from-directory "${output_html}" "${output_html.files_path}"
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9 </command>
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10
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11 <inputs>
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12 <conditional name="backend_database_source">
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13 <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?">
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14 <option value="history" selected="true">Use backend database from the history</option>
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15 <option value="cuffdiff_output">Build backend database using cuffdiff output</option>
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16 </param>
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17 <when value="cuffdiff_output">
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18 <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/>
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19 <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/>
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20 <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/>
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21 <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/>
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22 <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/>
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23 <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/>
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24 <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/>
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25 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/>
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26 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/>
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27 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/>
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28 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/>
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29 <param name="rebuild" type="hidden" value="TRUE"/>
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30 </when>
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31 <when value="history">
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32 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/>
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33 </when>
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34 </conditional>
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35 <repeat name="plots" title="Plots">
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36 <param name="width" type="text" value="1280" label="The width of the image"/>
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37 <param name="height" type="text" value="960" label="The height of the image"/>
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38 <conditional name="plot">
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39 <param name="type" type="select" label="Plot type">
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40 <option value="density" selected="true">Density</option>
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41 <option value="dispersion">Dispersion</option>
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42 <option value="fpkmSCV">Squared Coefficient of Variation</option>
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43 <option value="scatterMatrix">Scatter Matrix</option>
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44 <option value="boxplot">Boxplot</option>
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45 <option value="scatter">Scatter</option>
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46 <option value="volcano">Volcano</option>
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47 <option value="heatmap">Heatmap</option>
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48 <option value="cluster">Cluster</option>
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49 <option value="expressionplot">Expression Plot</option>
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50 <option value="expressionbarplot">Expression Bar Plot</option>
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51 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
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52 <option value="pca">Principal Component Analysis (PCA) Plot</option>
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53 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
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54 <option value="dendrogram">Dendrogram</option>
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55 </param>
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56 <when value="density">
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57 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
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58 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/>
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59 </when>
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60 <when value="mds">
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61 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
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62 </when>
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63 <when value="pca">
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64 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
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65 </when>
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66 <when value="maplot">
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67 <param name="x" type="text" label="Sample name 1"/>
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68 <param name="y" type="text" label="Sample name 2"/>
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69 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
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70 </when>
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71 <when value="dendrogram">
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72 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
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73 </when>
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74 <when value="dispersion">
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75 </when>
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76 <when value="fpkmSCV">
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77 </when>
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78 <when value="scatterMatrix">
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79 </when>
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80 <when value="boxplot">
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81 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
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82 </when>
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83 <when value="scatter">
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84 <param name="x" type="text" label="Sample name for x axis"/>
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85 <param name="y" type="text" label="Sample name for y axis"/>
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86 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
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87 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/>
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88 <conditional name="multiple_genes">
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89 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
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90 <when value="T">
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91 <param name="features" type="select" label="Expression levels to plot?">
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92 <option value="gene" selected="true">Genes</option>
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93 <option value="isoforms">Isoforms</option>
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94 <option value="tss">TSS</option>
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95 <option value="cds">CDS</option>
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96 </param>
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97 <repeat name="genes" title="Genes">
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98 <param name="gene_id" type="text" label="Gene ID"/>
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99 </repeat>
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100 </when>
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101 <when value="F"/>
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102 </conditional>
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103 </when>
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104 <when value="volcano">
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105 <param name="x" type="text" label="First sample name for comparison"/>
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106 <param name="y" type="text" label="Second sample name for comparison"/>
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107 <conditional name="multiple_genes">
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108 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
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109 <when value="T">
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110 <param name="features" type="select" label="Expression levels to plot?">
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111 <option value="gene" selected="true">Genes</option>
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112 <option value="isoforms">Isoforms</option>
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113 <option value="tss">TSS</option>
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114 <option value="cds">CDS</option>
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115 </param>
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116 <repeat name="genes" title="Genes">
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117 <param name="gene_id" type="text" label="Gene ID"/>
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118 </repeat>
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119 </when>
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120 <when value="F"/>
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121 </conditional>
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122 </when>
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123 <when value="heatmap">
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124 <param name="features" type="select" label="Expression levels to plot?">
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125 <option value="gene" selected="true">Genes</option>
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126 <option value="isoforms">Isoforms</option>
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127 <option value="tss">TSS</option>
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128 <option value="cds">CDS</option>
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129 </param>
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130 <repeat name="genes" title="Genes">
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131 <param name="gene_id" type="text" label="Gene ID"/>
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132 </repeat>
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133 <param name="clustering" type="select" label="Cluster by">
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134 <option value="row">Row</option>
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135 <option value="column">Column</option>
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136 <option value="both" selected="true">Both</option>
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137 <option value="none">None</option>
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138 </param>
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139 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
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140 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
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141 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
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142 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/>
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143 </when>
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144 <when value="cluster">
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145 <param name="features" type="select" label="Expression levels to plot?">
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146 <option value="gene" selected="true">Genes</option>
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147 <option value="isoforms">Isoforms</option>
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148 <option value="tss">TSS</option>
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149 <option value="cds">CDS</option>
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150 </param>
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151 <repeat name="genes" title="Genes">
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152 <param name="gene_id" type="text" label="Gene ID"/>
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153 </repeat>
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154 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/>
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155 <param name="iter_max" type="text" value="100" label="Max iterations"/>
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156 </when>
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157 <when value="expressionplot">
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158 <param name="features" type="select" label="Expression levels to plot?">
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159 <option value="gene" selected="true">Genes</option>
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160 <option value="isoforms">Isoforms</option>
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161 <option value="tss">TSS</option>
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162 <option value="cds">CDS</option>
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163 </param>
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164 <param name="gene_id" type="text" label="Gene ID"/>
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165 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
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166 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM
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167 values for each condition?"/>
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168 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
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169 </when>
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170 <when value="expressionbarplot">
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171 <param name="features" type="select" label="Expression levels to plot?">
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172 <option value="gene" selected="true">Genes</option>
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173 <option value="isoforms">Isoforms</option>
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174 <option value="tss">TSS</option>
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175 <option value="cds">CDS</option>
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176 </param>
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177 <param name="gene_id" type="text" label="Gene ID"/>
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178 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
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179 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
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180 </when>
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181 </conditional>
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182 </repeat>
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183 </inputs>
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184 <stdio>
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185 <exit_code range="1:" level="fatal" description="CummerBund Error" />
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186 </stdio>
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187 <outputs>
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188 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
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189 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
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190 </data>
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191 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
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192 </outputs>
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193
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194 <requirements>
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195 <requirement type="binary">R</requirement>
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196 </requirements>
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197
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198 <!-->
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199 <tests>
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200 <test>
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201 <param name="" value=""/>
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202 <output name="" file=""/>
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203 </test>
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204 </tests>
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205 -->
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206 <configfiles>
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207 <configfile name="script_file">
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208
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209 ## Feature Selection ##
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210 get_features <- function(myGenes, f="gene") {
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211 if (f == "isoforms")
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212 return(isoforms(myGenes))
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213 else if (f == "tss")
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214 return(TSS(myGenes))
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215 else if (f == "cds")
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216 return(CDS(myGenes))
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217 else
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218 return(myGenes)
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219 }
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220
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221 ## Main Function ##
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222
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223 ## Load cummeRbund library
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224 library("cummeRbund")
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225
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226 ## Initialize cuff object
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227 cuff <- readCufflinks(dir = "",
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228 #if $backend_database_source.backend_database_selector == "cuffdiff_output":
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229 dbFile = "${output_database}",
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230 geneFPKM = "${genes_fpkm_tracking}",
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231 geneDiff = "${genes_exp}",
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232 isoformFPKM = "${isoforms_fpkm_tracking}",
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233 isoformDiff = "${isoforms_exp}",
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234 TSSFPKM = "${tss_groups_fpkm_tracking}",
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235 TSSDiff = "${tss_groups_exp}",
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236 CDSFPKM = "${cds_fpkm_tracking}",
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237 CDSExpDiff = "${cds_exp_diff}",
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238 CDSDiff = "${cds_diff}",
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239 promoterFile = "${promoters_diff}",
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240 splicingFile = "${splicing_diff}",
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241 rebuild = T)
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242 #else:
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243 dbFile = "${backend_database_source.input_database}",
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244 rebuild = F)
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245 #end if
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246
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247 #for $i, $p in enumerate($plots, start=1):
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248 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
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249 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
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250 tryCatch({
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251 ## Density plot ##
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252 #if $p.plot['type'] == "density":
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253 csDensity(genes(cuff),replicates=$p.plot.replicates)
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254
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255 ## Dispersion plot ##
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256 #elif $p.plot['type'] == "dispersion":
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257 dispersionPlot(genes(cuff))
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258
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259 ## Squared Coefficient of Variation plot ##
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260 #elif $p.plot['type'] == "fpkmSCV":
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261 fpkmSCVPlot(genes(cuff))
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262
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263 ## Scatter Matrix ##
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264 #elif $p.plot['type'] == "scatterMatrix":
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265 csScatterMatrix(genes(cuff))
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266
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267 ## Boxplot ##
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268 #elif $p.plot['type'] == "boxplot":
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269 csBoxplot(genes(cuff))
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270
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271 ## Scatter ##
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272 #elif $p.plot['type'] == "scatter":
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273 #if $p.plot.multiple_genes['multiple_genes_selector']:
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274 myGeneIds <- c()
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275 #for $g in $p.plot.multiple_genes['genes']:
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276 myGeneIds <- c(myGeneIds, "$g['gene_id']")
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277 #end for
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278 myGenes <- getGenes(cuff, myGeneIds)
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279 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
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280 #else
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281 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
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282 #end if
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283
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284 ## Volcano ##
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285 #elif $p.plot['type'] == "volcano":
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286 #if $p.plot.multiple_genes['multiple_genes_selector']:
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287 myGeneIds <- c()
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288 #for $g in $p.plot.multiple_genes['genes']:
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289 myGeneIds <- c(myGeneIds, "$g['gene_id']")
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290 #end for
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291 myGenes <- getGenes(cuff, myGeneIds)
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292 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}")
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293 #else
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294 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}")
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295 #end if
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296
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297 ## Heatmap ##
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298 #elif $p.plot['type'] == "heatmap":
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299 myGeneIds <- c()
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300 #for $g in $p.plot.genes:
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301 myGeneIds <- c(myGeneIds, "$g['gene_id']")
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302 #end for
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303 myGenes <- getGenes(cuff, myGeneIds)
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304 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}")
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305
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306 ## Cluster ##
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307 #elif $p.plot['type'] == "cluster":
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308 myGeneIds <- c()
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309 #for $g in $p.plot.genes:
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310 myGeneIds <- c(myGeneIds, "$g['gene_id']")
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311 #end for
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312 myGenes <- getGenes(cuff, myGeneIds)
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313 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}")
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314
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315 ## Expression Plot ##
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316 #elif $p.plot['type'] == "expressionplot":
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317 myGeneId <- "$p.plot.gene_id"
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318 myGenes <- getGenes(cuff, myGeneId)
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319 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}")
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320
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321 ## Expression Bar Plot ##
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322 #elif $p.plot['type'] == "expressionbarplot":
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323 myGeneId <- "$p.plot.gene_id"
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324 myGenes <- getGenes(cuff, myGeneId)
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325 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}")
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326
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327 ## MDS plot ##
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328 #elif $p.plot['type'] == "mds":
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329 MDSplot(genes(cuff),replicates=$p.plot.replicates)
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330
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331 ## PCA plot ##
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332 #elif $p.plot['type'] == "pca":
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333 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates)
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334
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335 ## MAplot plot ##
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336 #elif $p.plot['type'] == "maplot":
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337 MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count})
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338
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339 ## Dendogram plot ##
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340 #elif $p.plot['type'] == "dendrogram":
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341 csDendro(genes(cuff),replicates=$p.plot.replicates)
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342 #end if
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343
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344 },error = function(e) {paste("$p.plot['type'] failed: ", e)})
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345 devname = dev.off()
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346
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347 #end for
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348 </configfile>
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349 </configfiles>
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350
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351 <help>
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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 </help>
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354
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355 </tool>
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