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comparison assembly_post_processor.xml @ 37:cc4dba9f6ecd draft

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author greg
date Fri, 07 Apr 2017 08:34:58 -0400
parents 2553e8e46fab
children 9b5baf12bdbe
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36:2553e8e46fab 37:cc4dba9f6ecd
1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="0.4.0"> 1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="0.4.0">
2 <description>post-processes de novo transcriptome assembly</description> 2 <description>post-processes de novo transcriptome assembly</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <stdio> 6 <expand macro="requirements_assembly_post_processor" />
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 AssemblyPostProcesser 10 AssemblyPostProcesser
17 --transcripts '$input' 11 --transcripts '$input'
18 --prediction_method $prediction_method_cond.prediction_method 12 --prediction_method $prediction_method_cond.prediction_method
151 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12]. 145 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
152 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp. 146 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
153 147
154 </help> 148 </help>
155 <citations> 149 <citations>
156 <citation type="bibtex"> 150 <expand macro="citation1" />
157 @misc{None,
158 journal = {None},
159 author = {1. Wafula EK},
160 title = {Manuscript in preparation},
161 year = {None},
162 url = {https://github.com/dePamphilis/PlantTribes},}
163 </citation>
164 <citation type="bibtex"> 151 <citation type="bibtex">
165 @article{Honaas2016, 152 @article{Honaas2016,
166 journal = {PloS one}, 153 journal = {PloS one},
167 author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH}, 154 author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH},
168 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome}, 155 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},