comparison assembly_post_processor.xml @ 15:ff5c714e01d1 draft

Uploaded

14:b468a86f87d9

<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="0.4">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <stdio>

        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
        <![CDATA[
            AssemblyPostProcesser
            --transcripts "$input"
            --prediction_method $prediction_method_cond.prediction_method
            #if str($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_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
                    --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
                    --method "$options_type.target_gene_family_assembly_cond.method"
                #end if
                --gap_trimming $options_type.gap_trimming
                #if str($options_type.strand_specific) == 'yes':
                    --strand_specific
                #end if

    </outputs>
    <tests>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta" />
            <param name="prediction_method" value="transdecoder" />
            <param name="options_type_selector" value="basic" />
            <output_collection name="transcripts" type="list">
                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/>
                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta" />
            <param name="prediction_method" value="transdecoder" />

            <param name="min_length" value="200" />
            <output_collection name="transcripts" type="list">
                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
            </output_collection>
        </test>
    </tests>

            <citation type="bibtex">
                @unpublished{None,
                author = {Eric Wafula},
                title = {None},
                year = {None},
                eprint = {None},
                url = {None}
            }</citation>
    </citations>
</tool>

15:ff5c714e01d1

<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>

        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
        <![CDATA[
            #import os
            AssemblyPostProcesser
            --transcripts '$input'
            --prediction_method $prediction_method_cond.prediction_method
            #if str($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':
                    #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
                    #set scaffold_dir = $os.path.split($scaffold_path)[0]
                    #set scaffold = $os.path.split($scaffold_path)[1]
                    --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
                    --scaffold_dir '$scaffold_dir'
                    --scaffold '$scaffold'
                    --method '$options_type.target_gene_family_assembly_cond.method'
                #end if
                --gap_trimming $options_type.gap_trimming
                #if str($options_type.strand_specific) == 'yes':
                    --strand_specific
                #end if

    </outputs>
    <tests>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta" />
            <param name="prediction_method" value="transdecoder" />
            <output_collection name="transcripts" type="list">
                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/>
                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta" />
            <param name="prediction_method" value="transdecoder" />

            <param name="min_length" value="200" />
            <output_collection name="transcripts" type="list">
                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/>
                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
            </output_collection>
        </test>
    </tests>

            <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>