comparison assembly_post_processor.xml @ 24:a39def7197cf draft

Uploaded

23:fa95f44f2e1a

<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.4">
    <description>into putative coding sequences</description>
    <requirements>
        <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <stdio>

            #if str($prediction_method_cond.prediction_method) == 'estscan':
                --score_matrices '$score_matrices'
            #end if
            #if str($options_type.options_type_selector) == 'advanced':
                #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
                    --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
                    --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
                    --method '$options_type.target_gene_family_assembly_cond.method'
                #end if
                --gap_trimming $options_type.gap_trimming

 * **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                @unpublished{None,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},
                url = {https://github.com/dePamphilis/PlantTribes}
            }</citation>
            <citation type="bibtex">
                @published{Proc Int Conf Intell Syst Mol Biol,
                author = {Iseli C, Jongeneel CV, Bucher P.},
                title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
                year = {1999},
                url = {http://estscan.sourceforge.net/}
            }</citation>
            <citation type="doi">10.1038/nprot.2013.084</citation>
            <citation type="doi">10.1109/tcbb.2013.68</citation>
    </citations>
</tool>

24:a39def7197cf

<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.4.0">
    <description>into putative coding sequences</description>
    <requirements>
        <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <stdio>

            #if str($prediction_method_cond.prediction_method) == 'estscan':
                --score_matrices '$score_matrices'
            #end if
            #if str($options_type.options_type_selector) == 'advanced':
                #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
                    --config_dir '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
                    --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
                    --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
                    --method '$options_type.target_gene_family_assembly_cond.method'
                #end if
                --gap_trimming $options_type.gap_trimming

 * **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},
            url = {https://github.com/dePamphilis/PlantTribes}
        }</citation>
        <citation type="bibtex">
            @published{Proc Int Conf Intell Syst Mol Biol,
            author = {Iseli C, Jongeneel CV, Bucher P.},
            title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
            year = {1999},
            url = {http://estscan.sourceforge.net/}
        }</citation>
        <citation type="doi">10.1038/nprot.2013.084</citation>
        <citation type="doi">10.1109/tcbb.2013.68</citation>
        <citation type="bibtex">
            @unpublished{None,
            author = {None},
            title = {HMMER 3.1+ hmmscan search sequence(s) against a profile database},
            year = {2013},
            url = {http://hmmer.org/}
        }</citation>
        <citation type="bibtex">
            @published{Genome Research,
            author = {Huang X, Madan A},
            title = {CAP3: A DNA sequence assembly program},
            year = {1999},
            url = {http://seq.cs.iastate.edu/cap3.html}
        }</citation>
    </citations>
</tool>