|
0
|
1 <tool id="export2graphlan" name="export2graphlan" version="1.0.0">
|
|
|
2 <description>Export to Graphlan</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 export2graphlan.py
|
|
|
5 -i $inp_data
|
|
|
6 -o $out_data
|
|
|
7 -t $output_tree_file
|
|
|
8 -a $output_annot_file
|
|
18
|
9
|
|
0
|
10 --annotations $export_annotations
|
|
|
11 --external_annotations $export_external_annotations
|
|
14
|
12 --background_levels $background_levels
|
|
17
|
13 #if $str($background_clades) != " ":
|
|
16
|
14 --background_clades $background_clades
|
|
|
15 #end if
|
|
18
|
16 #if $str($background_colors) != " ":
|
|
|
17 --background_colors $background_colors
|
|
|
18 #end if
|
|
|
19 #if $str($export_title) != " ":
|
|
|
20 --title $export_title
|
|
|
21 #end if
|
|
|
22 --title_font_size $title_font_size
|
|
|
23 --def_clade_size $def_clade_size
|
|
|
24 --min_clade_size $min_clade_size
|
|
|
25 --max_clade_size $max_clade_size
|
|
20
|
26 --def_font_size $def_font_size
|
|
|
27 --min_font_size $min_font_size
|
|
|
28 --max_font_size $max_font_size
|
|
|
29 --annotation_legend_font_size $annotation_legend_font_size
|
|
|
30 --abundance_threshold $abundance_threshold
|
|
0
|
31 --skip_rows 1,2
|
|
|
32 </command>
|
|
|
33
|
|
|
34 <inputs>
|
|
19
|
35 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse" help="This is the file that was used as input for Lefse"/>
|
|
|
36 <param format="lefse_internal_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/>
|
|
14
|
37 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
|
|
|
38 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
|
|
|
39 <param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>
|
|
15
|
40 <param name="background_clades" type="text" format="text" label="Background Clades" value=" " />
|
|
18
|
41 <param name="background_colors" type="text" format="text" label="Background Colors" value=" " />
|
|
|
42 <param name="export_title" type="text" format="text" label="Title" value=" "/>
|
|
|
43 <param name="title_font_size" type="integer" size="4" value="15" label="Title font size"/>
|
|
|
44 <param name="def_clade_size" type="integer" size="4" value="0" label="Default Clade size"/>
|
|
|
45 <param name="min_clade_size" type="integer" size="4" value="20" label="Minimum Clade size that are Biomarkers"/>
|
|
|
46 <param name="max_clade_size" type="integer" size="4" value="200" label="Maximum Clade size that are Biomarkers"/>
|
|
20
|
47 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/>
|
|
|
48 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/>
|
|
|
49 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/>
|
|
|
50 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/>
|
|
|
51 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
|
|
|
52
|
|
14
|
53
|
|
0
|
54 </inputs>
|
|
|
55 <outputs>
|
|
|
56 <data name="output_annot_file" format="circl" />
|
|
|
57 <data name="output_tree_file" format="circl" />
|
|
|
58 </outputs>
|
|
|
59
|
|
|
60 <help>
|
|
|
61 Overview
|
|
|
62 ========
|
|
1
|
63 **export2graphlan** is an *OPTIONAL* tool that automatically convert **LEfSe**, **MetaPhlAn2**, and **HUMAnN** input and/or output files, to **GraPhlAn**. Input file can be also given in BIOM (both 1 and 2) format.
|
|
0
|
64
|
|
1
|
65 The aim of this tool is to support biologists, helping them by provide the tree and the annotation file for GraPhlAn, automatically.
|
|
|
66
|
|
|
67 Input files
|
|
|
68 -----------
|
|
|
69
|
|
|
70 As shown in the image below, export2graphlan can work with just one of the following files or with both of them.
|
|
|
71
|
|
|
72 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value.
|
|
|
73
|
|
|
74 * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers.
|
|
|
75
|
|
18
|
76 Input parameters6666
|
|
4
|
77 --------------------
|
|
3
|
78
|
|
4
|
79 --annotations ANNOTATIONS
|
|
1
|
80 List which levels should be annotated in the tree. Use
|
|
|
81 a comma separate values form, e.g.,
|
|
|
82 --annotation_levels 1,2,3. Default is None
|
|
4
|
83 --external_annotations EXTERNAL_ANNOTATIONS
|
|
1
|
84 List which levels should use the external legend for
|
|
|
85 the annotation. Use a comma separate values form,
|
|
|
86 e.g., --annotation_levels 1,2,3. Default is None
|
|
|
87 --background_levels BACKGROUND_LEVELS
|
|
|
88 List which levels should be highlight with a shaded
|
|
|
89 background. Use a comma separate values form, e.g.,
|
|
|
90 --background_levels 1,2,3
|
|
|
91 --background_clades BACKGROUND_CLADES
|
|
|
92 Specify the clades that should be highlight with a
|
|
|
93 shaded background. Use a comma separate values form
|
|
|
94 and surround the string with " if it contains spaces.
|
|
|
95 Example: --background_clades "Bacteria.Actinobacteria,
|
|
|
96 Bacteria.Bacteroidetes.Bacteroidia,
|
|
|
97 Bacteria.Firmicutes.Clostridia.Clostridiales"
|
|
|
98 --background_colors BACKGROUND_COLORS
|
|
|
99 Set the color to use for the shaded background. Colors
|
|
|
100 can be either in RGB or HSV (using a semi-colon to
|
|
|
101 separate values, surrounded with ()) format. Use a
|
|
|
102 comma separate values form and surround the string
|
|
|
103 with " if it contains spaces. Example:
|
|
|
104 --background_colors "#29cc36, (150; 100; 100), (280;
|
|
|
105 80; 88)"
|
|
|
106 --title TITLE If specified set the title of the GraPhlAn plot.
|
|
|
107 Surround the string with " if it contains spaces,
|
|
|
108 e.g., --title "Title example"
|
|
|
109 --title_font_size TITLE_FONT_SIZE
|
|
|
110 Set the title font size. Default is 15
|
|
|
111 --def_clade_size DEF_CLADE_SIZE
|
|
|
112 Set a default size for clades that are not found as
|
|
|
113 biomarkers by LEfSe. Default is 10
|
|
|
114 --min_clade_size MIN_CLADE_SIZE
|
|
|
115 Set the minimum value of clades that are biomarkers.
|
|
|
116 Default is 20
|
|
|
117 --max_clade_size MAX_CLADE_SIZE
|
|
|
118 Set the maximum value of clades that are biomarkers.
|
|
|
119 Default is 200
|
|
|
120 --def_font_size DEF_FONT_SIZE
|
|
|
121 Set a default font size. Default is 10
|
|
|
122 --min_font_size MIN_FONT_SIZE
|
|
|
123 Set the minimum font size to use. Default is 8
|
|
|
124 --max_font_size MAX_FONT_SIZE
|
|
|
125 Set the maximum font size. Default is 12
|
|
|
126 --annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE
|
|
|
127 Set the font size for the annotation legend. Default
|
|
|
128 is 10
|
|
|
129 --abundance_threshold ABUNDANCE_THRESHOLD
|
|
|
130 Set the minimun abundace value for a clade to be
|
|
|
131 annotated. Default is 20.0
|
|
|
132 --most_abundant MOST_ABUNDANT
|
|
|
133 When only lefse_input is provided, you can specify how
|
|
|
134 many clades highlight. Since the biomarkers are
|
|
|
135 missing, they will be chosen from the most abundant
|
|
|
136 --least_biomarkers LEAST_BIOMARKERS
|
|
|
137 When only lefse_input is provided, you can specify the
|
|
|
138 minimum number of biomarkers to extract. The taxonomy
|
|
|
139 is parsed, and the level is choosen in order to have
|
|
|
140 at least the specified number of biomarkers
|
|
|
141 --discard_otus If specified the OTU ids will be discarde from the
|
|
|
142 taxonmy. Default behavior keep OTU ids in taxonomy
|
|
|
143 --internal_levels If specified sum-up from leaf to root the abundances
|
|
|
144 values. Default behavior do not sum-up abundances on
|
|
|
145 the internal nodes
|
|
|
146
|
|
|
147 input parameters:
|
|
6
|
148 You need to provide at least LEfSe input data
|
|
3
|
149 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT
|
|
6
|
150
|
|
1
|
151 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT
|
|
|
152
|
|
|
153 output parameters:
|
|
13
|
154
|
|
1
|
155 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn
|
|
13
|
156
|
|
9
|
157 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation
|
|
7
|
158
|
|
1
|
159 Input data matrix parameters:
|
|
|
160 --sep SEP
|
|
9
|
161 --out_table OUT_TABLE : This is where to write the processed data matrix to file
|
|
12
|
162
|
|
11
|
163 --fname_row FNAME_ROW : Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)
|
|
12
|
164
|
|
1
|
165 --sname_row SNAME_ROW
|
|
11
|
166 column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
|
|
1
|
167 --metadata_rows METADATA_ROWS
|
|
|
168 Row numbers to use as metadata[default None, meaning
|
|
|
169 no metadata
|
|
|
170 --skip_rows SKIP_ROWS
|
|
|
171 Row numbers to skip (0-indexed, comma separated) from
|
|
|
172 the input file[default None, meaning no rows skipped
|
|
|
173 --sperc SPERC Percentile of sample value distribution for sample
|
|
|
174 selection
|
|
|
175 --fperc FPERC Percentile of feature value distribution for sample
|
|
|
176 selection
|
|
|
177 --stop STOP Number of top samples to select (ordering based on
|
|
|
178 percentile specified by --sperc)
|
|
|
179 --ftop FTOP Number of top features to select (ordering based on
|
|
|
180 percentile specified by --fperc)
|
|
|
181 --def_na DEF_NA Set the default value for missing values [default None
|
|
|
182 which means no replacement]
|
|
|
183
|
|
|
184 Integration
|
|
|
185 ===========
|
|
|
186
|
|
|
187 A graphical representation of how **export2graphlan** can be integrated in the analysis pipeline:
|
|
0
|
188
|
|
|
189 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
|
|
1
|
190 :height: 672
|
|
|
191 :width: 800
|
|
0
|
192
|
|
1
|
193 Want to know more?
|
|
|
194 ==================
|
|
0
|
195
|
|
2
|
196 If you want to know more about **export2graphlan** please have a look at the tutorial
|
|
0
|
197 </help>
|
|
|
198 </tool>
|
