Mercurial > repos > greg > plant_tribes_ks_distribution
comparison ks_distribution.xml @ 0:c5846258c458 draft
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author | greg |
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date | Thu, 08 Jun 2017 12:55:49 -0400 |
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children | 56f42cc1dd58 |
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1 <tool id="ks_distribution" name="KsDistribution" version="1.0.0"> | |
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> | |
6 <expand macro="requirements_ks_distribution" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 Rscript $__tool_directory__/ks_distribution.R | |
9 -k '$input' | |
10 -c '$components' | |
11 -o '$output' | |
12 ]]></command> | |
13 <inputs> | |
14 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" /> | |
15 <param name="components" format="tabular" type="data" label="Significant components" /> | |
16 </inputs> | |
17 <outputs> | |
18 <data name="output" format="pdf"/> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="input" value="kaks_input1.tabular" ftype="tabular" /> | |
23 <param name="components" value="components.tabular" ftype="tabular" /> | |
24 <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> | |
25 </test> | |
26 </tests> | |
27 <help> | |
28 **What it does** | |
29 | |
30 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of | |
31 genome-scale gene families and transcriptomes. This tool uses the analysis results produced by the KaKsAnalysis tool to plot the | |
32 distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution. | |
33 | |
34 ----- | |
35 | |
36 **Options** | |
37 | |
38 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history. | |
39 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history. | |
40 </help> | |
41 <citations> | |
42 <expand macro="citation1" /> | |
43 <citation type="bibtex"> | |
44 @article{Wall2008, | |
45 journal = {Nucleic Acids Research}, | |
46 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS}, | |
47 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants}, | |
48 year = {2008}, | |
49 volume = {36}, | |
50 number = {suppl 1}, | |
51 pages = {D970-D976},} | |
52 </citation> | |
53 <citation type="bibtex"> | |
54 @article{Altschul1990, | |
55 journal = {Journal of molecular biology} | |
56 author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ}, | |
57 title = {Basic local alignment search tool}, | |
58 year = {1990}, | |
59 volume = {215}, | |
60 number = {3}, | |
61 pages = {403-410},} | |
62 </citation> | |
63 <citation type="bibtex"> | |
64 @article{Katoh2013, | |
65 journal = {Molecular biology and evolution}, | |
66 author = {4. Katoh K, Standley DM}, | |
67 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability}, | |
68 year = {2013}, | |
69 volume = {30}, | |
70 number = {4}, | |
71 pages = {772-780},} | |
72 </citation> | |
73 <citation type="bibtex"> | |
74 @article{Yang2007, | |
75 journal = {Molecular biology and evolution}, | |
76 author = {5. Yang Z}, | |
77 title = {PAML 4: phylogenetic analysis by maximum likelihood}, | |
78 year = {2007}, | |
79 volume = {24}, | |
80 number = {8}, | |
81 pages = {1586-1591},} | |
82 </citation> | |
83 <citation type="bibtex"> | |
84 @article{Cui2006, | |
85 journal = {Genome Research}, | |
86 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}, | |
87 title = {Widespread genome duplications throughout the history of flowering plants}, | |
88 year = {2006}, | |
89 volume = {16}, | |
90 number = {6}, | |
91 pages = {738-749},} | |
92 </citation> | |
93 <citation type="bibtex"> | |
94 @article{McLachlan1999, | |
95 journal = {Journal of Statistical Software}, | |
96 author = {7. McLachlan GJ, Peel D, Basford KE, Adams P}, | |
97 title = {The EMMIX software for the fitting of mixtures of normal and t-components}, | |
98 year = {1999}, | |
99 volume = {4}, | |
100 number = {2}, | |
101 pages = {1-14},} | |
102 </citation> | |
103 </citations> | |
104 </tool> | |
105 |