comparison assembly_post_processor.xml @ 5:31673ee3734f draft

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4:842c77ce5fd8

<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="1.0.0">
    <description>pipeline</description>
    <requirements>
        <requirement type="package" version="0.2">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <!-- In case the return code has not been set properly check stderr too -->

            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It post-processes de novo assembly
transcripts into putative coding sequences and their corresponding amino acid translations.

-----

**Options**

 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
 * **Target gene family assembly?** - Select yes to target gene families to assemble.
 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.  The next version of this tool will use a dynamic select list for this feature.
 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
 * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
 * **Remove gappy sites in alignments** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
 * **De novo transcriptome assembly was performed with strand-specific library?** - Select yes if de novo transcriptome assembly was performed with strand-specific library.
 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.
 
    </help>
    <citations>
            <citation type="bibtex">
                @unpublished{None,
                author = {None},
                title = {None},
                year = {None},
                eprint = {None},
                url = {None}
            }</citation>

5:31673ee3734f

<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3">
    <description>into putative coding sequences</description>
    <requirements>
        <requirement type="package" version="0.3">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <!-- In case the return code has not been set properly check stderr too -->

            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It postprocesses de novo assembly
transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families.

-----

**Options**

 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.
 
    </help>
    <citations>
            <citation type="bibtex">
                @unpublished{None,
                author = {Eric Wafula},
                title = {None},
                year = {None},
                eprint = {None},
                url = {None}
            }</citation>