comparison assembly_post_processor.xml @ 37:cc4dba9f6ecd draft

Uploaded

36:2553e8e46fab

<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="0.4.0">
    <description>post-processes de novo transcriptome assembly</description>
    <requirements>
        <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
        <![CDATA[
            AssemblyPostProcesser
            --transcripts '$input'
            --prediction_method $prediction_method_cond.prediction_method

 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.

    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {1. Wafula EK},
            title = {Manuscript in preparation},
            year = {None},
            url = {https://github.com/dePamphilis/PlantTribes},}
        </citation>
        <citation type="bibtex">
            @article{Honaas2016,
            journal = {PloS one},
            author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH},
            title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},

37:cc4dba9f6ecd

<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="0.4.0">
    <description>post-processes de novo transcriptome assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_assembly_post_processor" />
    <expand macro="stdio" />
    <command>
        <![CDATA[
            AssemblyPostProcesser
            --transcripts '$input'
            --prediction_method $prediction_method_cond.prediction_method

 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.

    </help>
    <citations>
        <expand macro="citation1" />
        <citation type="bibtex">
            @article{Honaas2016,
            journal = {PloS one},
            author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH},
            title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome},