4
|
1 <tool id="ks_distribution" name="KsDistribution" version="@WRAPPER_VERSION@.3.0">
|
0
|
2 <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
|
|
3 <macros>
|
|
4 <import>macros.xml</import>
|
|
5 </macros>
|
4
|
6 <requirements>
|
|
7 <requirement type="package" version="1.3.2">r-optparse</requirement>
|
|
8 </requirements>
|
0
|
9 <command detect_errors="exit_code"><![CDATA[
|
2
|
10 Rscript '$__tool_directory__/ks_distribution.R'
|
0
|
11 -k '$input'
|
|
12 -c '$components'
|
1
|
13 -n $components.metadata.number_comp
|
0
|
14 -o '$output'
|
1
|
15 #if str($choose_colors_cond.choose_colors) == 'yes':
|
|
16 #set specified_colors = list()
|
|
17 #for $selection in $choose_colors_cond.colors:
|
|
18 $specified_colors.append(str($selection.color))
|
|
19 #end for
|
|
20 #set specified_colors = ",".join($specified_colors)
|
|
21 -s '$specified_colors'
|
|
22 #end if
|
0
|
23 ]]></command>
|
|
24 <inputs>
|
|
25 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
|
4
|
26 <param name="components" format="tabular" type="data" label="Significant components" />
|
1
|
27 <conditional name="choose_colors_cond">
|
|
28 <param name="choose_colors" type="select" label="Choose colors for significant components">
|
|
29 <option value="no" selected="true">No</option>
|
|
30 <option value="yes">Yes</option>
|
|
31 </param>
|
|
32 <when value="no" />
|
|
33 <when value="yes">
|
|
34 <repeat name="colors" title="Component colors" min="1">
|
|
35 <param name="color" type="select" label="Color">
|
|
36 <option value="red" selected="True">red</option>
|
|
37 <option value="green">green</option>
|
|
38 <option value="blue">blue</option>
|
|
39 <option value="yellow">yellow</option>
|
|
40 <option value="darkorange">dark orange</option>
|
|
41 <option value="black">black</option>
|
|
42 </param>
|
|
43 </repeat>
|
|
44 </when>
|
|
45 </conditional>
|
0
|
46 </inputs>
|
|
47 <outputs>
|
|
48 <data name="output" format="pdf"/>
|
|
49 </outputs>
|
|
50 <tests>
|
|
51 <test>
|
|
52 <param name="input" value="kaks_input1.tabular" ftype="tabular" />
|
1
|
53 <param name="components" value="components.ptkscmp" ftype="ptkscmp" />
|
0
|
54 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
|
|
55 </test>
|
|
56 </tests>
|
|
57 <help>
|
|
58 **What it does**
|
|
59
|
|
60 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
|
|
61 genome-scale gene families and transcriptomes. This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
|
|
62 distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
|
|
63
|
|
64 -----
|
|
65
|
|
66 **Options**
|
|
67
|
|
68 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
|
|
69 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
|
1
|
70 * **Choose colors for significant components** - select 'Yes' to specify component colors or 'No' for colors chosen randlomly.
|
|
71
|
|
72 * **Component colors** - select a color from the palette for each component (colors will be chosen randomly for unspecified components).
|
0
|
73 </help>
|
|
74 <citations>
|
|
75 <expand macro="citation1" />
|
|
76 <citation type="bibtex">
|
|
77 @article{Wall2008,
|
|
78 journal = {Nucleic Acids Research},
|
|
79 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
|
|
80 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
|
|
81 year = {2008},
|
|
82 volume = {36},
|
|
83 number = {suppl 1},
|
|
84 pages = {D970-D976},}
|
|
85 </citation>
|
|
86 <citation type="bibtex">
|
|
87 @article{Altschul1990,
|
|
88 journal = {Journal of molecular biology}
|
|
89 author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
|
|
90 title = {Basic local alignment search tool},
|
|
91 year = {1990},
|
|
92 volume = {215},
|
|
93 number = {3},
|
|
94 pages = {403-410},}
|
|
95 </citation>
|
|
96 <citation type="bibtex">
|
|
97 @article{Katoh2013,
|
|
98 journal = {Molecular biology and evolution},
|
|
99 author = {4. Katoh K, Standley DM},
|
|
100 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
|
|
101 year = {2013},
|
|
102 volume = {30},
|
|
103 number = {4},
|
|
104 pages = {772-780},}
|
|
105 </citation>
|
|
106 <citation type="bibtex">
|
|
107 @article{Yang2007,
|
|
108 journal = {Molecular biology and evolution},
|
|
109 author = {5. Yang Z},
|
|
110 title = {PAML 4: phylogenetic analysis by maximum likelihood},
|
|
111 year = {2007},
|
|
112 volume = {24},
|
|
113 number = {8},
|
|
114 pages = {1586-1591},}
|
|
115 </citation>
|
|
116 <citation type="bibtex">
|
|
117 @article{Cui2006,
|
|
118 journal = {Genome Research},
|
|
119 author = {6. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA},
|
|
120 title = {Widespread genome duplications throughout the history of flowering plants},
|
|
121 year = {2006},
|
|
122 volume = {16},
|
|
123 number = {6},
|
|
124 pages = {738-749},}
|
|
125 </citation>
|
|
126 <citation type="bibtex">
|
|
127 @article{McLachlan1999,
|
|
128 journal = {Journal of Statistical Software},
|
|
129 author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
|
|
130 title = {The EMMIX software for the fitting of mixtures of normal and t-components},
|
|
131 year = {1999},
|
|
132 volume = {4},
|
|
133 number = {2},
|
|
134 pages = {1-14},}
|
|
135 </citation>
|
|
136 </citations>
|
|
137 </tool>
|
|
138
|