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comparison kaks_analysis.xml @ 26:73db26d39092 draft

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author greg
date Tue, 11 Apr 2017 13:36:06 -0400
parents 2c1eb9d63558
children f174450ebc44
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25:2c1eb9d63558 26:73db26d39092
1 <tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="0.8.0"> 1 <tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="@WRAPPER_VERSION@.0">
2 <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description> 2 <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <stdio> 6 <expand macro="requirements_kaks_analysis" />
7 <!-- Anything other than zero is an error --> 7 <expand macro="stdio" />
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <!-- In case the return code has not been set propery check stderr too -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
14 <command> 8 <command>
15 <![CDATA[ 9 <![CDATA[
16 #set output_dir = 'kaksAnalysis_dir' 10 #set output_dir = 'kaksAnalysis_dir'
17 #set comparison = $comparison_cond.comparison 11 #set comparison = $comparison_cond.comparison
18 #if str($options_type.options_type_selector) == 'advanced': 12 #if str($options_type.options_type_selector) == 'advanced':
225 - **Lower limit of synonymous subsitutions (ks)** - Lower limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to reduce background noise from young paralogous pairs due to normal gene births and deaths in a genome. 219 - **Lower limit of synonymous subsitutions (ks)** - Lower limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to reduce background noise from young paralogous pairs due to normal gene births and deaths in a genome.
226 - **Upper limit of synonymous subsitutions (ks)** - Upper limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to exclude likey ancient paralogous pairs. 220 - **Upper limit of synonymous subsitutions (ks)** - Upper limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to exclude likey ancient paralogous pairs.
227 221
228 </help> 222 </help>
229 <citations> 223 <citations>
230 <citation type="bibtex"> 224 <expand macro="citation1" />
231 @article{None,
232 journal = {None},
233 author = {1. Wafula EK},
234 title = {Manuscript in preparation},
235 year = {None},
236 url = {https://github.com/dePamphilis/PlantTribes},}
237 </citation>
238 <citation type="doi">10.1093/bioinformatics/btw412</citation> 225 <citation type="doi">10.1093/bioinformatics/btw412</citation>
239 <citation type="doi">10.1186/1471-2105-10-421</citation> 226 <citation type="doi">10.1186/1471-2105-10-421</citation>
240 <citation type="doi">10.1093/molbev/msm088</citation> 227 <citation type="doi">10.1093/molbev/msm088</citation>
241 <citation type="doi">10.18637/jss.v004.i02</citation> 228 <citation type="doi">10.18637/jss.v004.i02</citation>
242 </citations> 229 </citations>