Mercurial > repos > george-weingart > lefse
comparison home/ubuntu/lefse_to_export/plot_features.xml @ 1:db64b6287cd6 draft
Modified datatypes
author | george-weingart |
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date | Wed, 20 Aug 2014 16:56:51 -0400 |
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0:e7cd19afda2e | 1:db64b6287cd6 |
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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> |