comparison assembly_post_processor.xml @ 3:d651432961fb draft

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2:4eb05d406410

                #end if
                --min_length $options_type.min_length
            #end if
            --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
            --num_threads \${GALAXY_SLOTS:-4}
        ]]>
    </command>
    <inputs>
        <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">

                            <option value="orthofinder">OrthoFinder</option>
                            <option value="orthomcl">OrthoMCL</option>
                        </param>
                    </when>
                </conditional>
                <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove gappy sites in alignments" help="0.1 removes sites with 90% gaps"/>
                <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?">
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>
                </param>
                <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?">

3:d651432961fb

                #end if
                --min_length $options_type.min_length
            #end if
            --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
            --num_threads \${GALAXY_SLOTS:-4}
            --no_config_override
        ]]>
    </command>
    <inputs>
        <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">

                            <option value="orthofinder">OrthoFinder</option>
                            <option value="orthomcl">OrthoMCL</option>
                        </param>
                    </when>
                </conditional>
                <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/>
                <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?">
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>
                </param>
                <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?">