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1 <tool id="LEfSe_fea" name="F) Plot Differential Features" version="1.0">
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2 <description></description>
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3 <command interpreter="python">plot_features.py $inp_data $inp_res $arch --title_font_size $graphical.title_font_size --background_color $graphical.background_color --class_label_pos $graphical.class_label_pos --class_font_size $graphical.class_font_size --top $graphical.top --bot $graphical.bot --font_size $graphical.font_size --width $graphical.width --height $graphical.height -f $feature_set --archive "zip" --format $for --dpi $dpi --subcl_mean $graphical.subcl_mean --subcl_median $graphical.subcl_median </command>
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4 <inputs>
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5 <page>
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6 <param format="lefse" name="inp_data" type="data" label="The formatted datasets" help=""/>
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7 <param format="lefse_res" name="inp_res" type="data" label="The LEfSe output" help=""/>
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8
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9 <param name="feature_set" type="select" label="Do you want to plot all features or only those detected as biomarkers?">
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10 <option value="diff" selected="diff">Biomarkers only</option>
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11 <option value="all">All</option>
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12 </param>
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13
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14
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15 <conditional name="graphical">
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16 <param name="graphical_choice" type="select" label="Set some graphical options to personalize the output">
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17 <option value="d" selected='True'>Default</option>
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18 <option value="a">Advanced</option>
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19 </param>
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20 <when value="d">
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21 <param name="top" type="hidden" value="-1.0" />
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22 <param name="bot" type="hidden" value="0.0" />
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23 <param name="title_font_size" type="hidden" value="14" />
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24 <param name="class_font_size" type="hidden" value="12" />
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25 <param name="font_size" type="hidden" value="8" />
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26 <param name="width" type="hidden" value="7.0" />
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27 <param name="height" type="hidden" value="4.0" />
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28 <param name="background_color" type="hidden" value="w" />
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29 <param name="width" type="hidden" value="7.0" />
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30 <param name="height" type="hidden" value="4.0" />
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31 <param name="class_label_pos" type="hidden" value="up" />
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32 <param name="subcl_mean" type="hidden" value="y" />
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33 <param name="subcl_median" type="hidden" value="y" />
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34 </when>
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35
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36 <when value="a">
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37 <param name="top" type="float" size="2" value="-1.0" label="Set the maximum y value (-1.0 means automatic maximum setting based on maximum class median)"/>
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38 <param name="bot" type="float" size="2" value="0.0" label="Set the minimum y value (-1.0 means automatic minimum setting based on minimum class median)"/>
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39 <param name="title_font_size" type="integer" size="2" value="14" label="Title font size"/>
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40 <param name="class_font_size" type="integer" size="2" value="12" label="Class font size"/>
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41 <param name="font_size" type="integer" size="2" value="8" label="Size of subclasses names and y values"/>
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42 <param name="width" type="float" size="2" value="7.0" label="Width of the plot"/>
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43 <param name="height" type="float" size="2" value="4.0" label="Height of the plot"/>
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44 <param name="background_color" type="select" label="Background color">
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45 <option value="w" selected='True'>White</option>
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46 <option value="k">Black</option>
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47 </param>
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48 <param name="class_label_pos" type="select" label="Class label position">
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49 <option value="up" selected='True'>Top</option>
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50 <option value="down">Bottom</option>
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51 </param>
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52 <param name="subcl_mean" type="select" label="Whether to plot the subclass means (straight line)">
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53 <option value="y" selected='True'>Yes</option>
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54 <option value="n">No</option>
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55 </param>
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56 <param name="subcl_median" type="select" label="Whether to plot the subclass medians (dotted line)">
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57 <option value="y" selected='True'>Yes</option>
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58 <option value="n">No</option>
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59 </param>
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60
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61 </when>
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62
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63 </conditional>
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64
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65 <param name="for" type="select" label="Output format">
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66 <option value="png" selected="png">png</option>
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67 <option value="svg">svg</option>
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68 <option value="pdf">pdf</option>
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69 </param>
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70 <param name="dpi" type="select" label="Set the dpi resolution of the output">
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71 <option value="72">72</option>
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72 <option value="150" selected="True">150</option>
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73 <option value="300">300</option>
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74 <option value="600">600</option>
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75 <option value="1200">1200</option>
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76 </param>
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77
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78 </page>
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79 </inputs>
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80 <outputs>
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81 <data format="zip" name="arch" >
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82 </data>
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/>
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87 <param name="maf_source" value="cached"/>
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88 <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/>
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89 <param name="species" value="hg18,mm8"/>
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90 <param name="overwrite_with_gaps" value="True"/>
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91 <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" />
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92 </test>
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93 <test>
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94 <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
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95 <param name="maf_source" value="cached"/>
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96 <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/>
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97 <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
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98 <param name="overwrite_with_gaps" value="True"/>
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99 <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" />
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100 </test>
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101 <test>
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102 <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
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103 <param name="maf_source" value="user"/>
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104 <param name="maf_file" value="5.maf"/>
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105 <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
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106 <param name="overwrite_with_gaps" value="True"/>
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107 <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" />
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108 </test>
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109 </tests>
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110 <help>
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111 **What it does**
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112
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113 This module plots the raw data of the features detected by LEfSe as biomarkers as abundance histograms
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114 with class and subclass information. The features are exported as images and
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115 the user can download all the images in a .zip archive. It is also possible to
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116 export all the features (instead of the biomarkers only). For exporting or
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117 analyzing few features only the "Plot One Feature" module is recommended.
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118
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119 ------
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120
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121 **Input format**
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122
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123 The module accepts two datasets: the data formatted with the "Format Input for
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124 LEfSe" module and the output of the LEfSe analysis. Both datasets are necessary
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125 to run the module.
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126
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127 ------
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128
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129 **Output format**
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130
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131 The module generates zip archives containing images in png, svg or pdf format.
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132
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133 ------
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134
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135 **Advanced parameter settings**
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136
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137 *Graphical options*
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138 * Set the maximum y value: -1 means automatic parameter setting that is computed as the minimum between the highest abundance value and three times the highest subclass median.
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139 * Set the minimum y value: -1 means automatic parameter setting that is computed as the maximum between 0 and the 90% of the smallest abundance value.
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140 * Title font size: set the font size of the title only.
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141 * Class font size: set the font of the legend for the class names and colors.
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142 * Size of subclasses names and y values: set the font size for the axis labels.
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143 * Width of the plot: horizontal size (in inches) of the plot.
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144 * Height of the plot: vertical size (in inches) of the plot.
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145 * Background color: whether to generate plots with black or white backgrounds, adjusting properly the other colors.
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146 * Class label position: whether to place the class labels on the top or on the bottom of the plot.
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147 * Plot subclass means (straight line): whether to plot the subclass means with straight horizontal lines.
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148 * Plot subclass medians (dotted line): whether to plot the subclass medians with dotted horizontal lines.
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149
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150 ------
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151
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152 **Examples**
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153
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154 Please see the examples reported for the "Plot One Feature" module (E). This
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155 module just produces multiple plots in the same way and compresses them into a
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156 .zip archive.
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157
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158 </help>
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159 </tool>
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