comparison assembly_post_processor.xml @ 6:c197d5306cd6 draft

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5:2732db7dd0ef

        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set output_dir = 'assemblyPostProcessing_dir'
AssemblyPostProcessor
--transcripts '$input'
--prediction_method $prediction_method_cond.prediction_method

                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
                        <param name="scaffold" type="select" label="Gene family 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>
                        </param>
                        <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
                        <param name="min_coverage" type="float" value="0" min="0" max="1.0" label="Minimum alignment coverage"/>
                    </when>
                </conditional>
                <param name="strand_specific" type="select" label="Strand-specific assembly?">

6:c197d5306cd6

        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <code file="get_clustering_methods.py"/>
    <command detect_errors="exit_code"><![CDATA[
#set output_dir = 'assemblyPostProcessing_dir'
AssemblyPostProcessor
--transcripts '$input'
--prediction_method $prediction_method_cond.prediction_method

                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="orthogroups" format="tabular" type="data" label="Targeted gene families"/>
                        <expand macro="param_scaffold"/>
                        <expand macro="param_method"/>
                        <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
                        <param name="min_coverage" type="float" value="0" min="0" max="1.0" label="Minimum alignment coverage"/>
                    </when>
                </conditional>
                <param name="strand_specific" type="select" label="Strand-specific assembly?">