comparison assembly_post_processor.xml @ 10:db0c2baf176f draft

Uploaded

9:5a0a049d11aa

        <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 '$options_type.target_gene_family_assembly_cond.scaffold.path'
                    --scaffold '$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

                    <when value="no" />
                    <when value="yes">
                        <param name="orthogroups" format="tabular" type="data" label="List of orthogroup identifiers for target gene families to assemble"/>
                        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
                            <options from_data_table="plant_tribes_scaffolds" />
                            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
                        </param>
                        <param name="method" type="select" label="Protein clustering method">
                            <option value="gfam" selected="true">GFam</option>
                            <option value="orthofinder">OrthoFinder</option>
                            <option value="orthomcl">OrthoMCL</option>

            <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                @unpublished{None,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>

10:db0c2baf176f

        <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.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

                    <when value="no" />
                    <when value="yes">
                        <param name="orthogroups" format="tabular" type="data" label="List of orthogroup identifiers for target gene families to assemble"/>
                        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
                            <options from_data_table="plant_tribes_scaffolds" />
                            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
                        </param>
                        <param name="method" type="select" label="Protein clustering method">
                            <option value="gfam" selected="true">GFam</option>
                            <option value="orthofinder">OrthoFinder</option>
                            <option value="orthomcl">OrthoMCL</option>

            <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>