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