comparison assembly_post_processor.xml @ 86:126430ebebf7 draft

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85:b5aac0d2c99c

    </macros>
    <requirements>
        <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/assembly_post_processor.py'
--transcripts '$input'
--prediction_method $prediction_method_cond.prediction_method
#if str($prediction_method_cond.prediction_method) == 'estscan':
    --score_matrices '$score_matrices'
#end if

        --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
        --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
        --method '$target_gene_family_assembly_cond.method'
        --gap_trimming $target_gene_family_assembly_cond.gap_trimming
        --min_coverage $target_gene_family_assembly_cond.min_coverage
        --output_targeted_gene_families_stats '$output_targeted_gene_families_stats'
    #end if
    #if str($options_type.strand_specific) == 'yes':
        --strand_specific true
    #end if
    #if str($options_type.dereplicate) == 'yes':
        --dereplicate true
        --output_cleaned_nr_cds '$output_cleaned_nr_cds'
        --output_cleaned_nr_pep '$output_cleaned_nr_pep'
    #end if
    --min_length $options_type.min_length
#end if
--num_threads \${GALAXY_SLOTS:-4}
--output_cds '$output_cds'
--output_cleaned_cds '$output_cleaned_cds'
--output_cleaned_pep '$output_cleaned_pep'
--output_pep '$output_pep'
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">
            <param name="prediction_method" type="select" label="Coding regions prediction method">

86:126430ebebf7

    </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 $prediction_method_cond.prediction_method
#if str($prediction_method_cond.prediction_method) == 'estscan':
    --score_matrices '$score_matrices'
#end if

        --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
        --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
        --method '$target_gene_family_assembly_cond.method'
        --gap_trimming $target_gene_family_assembly_cond.gap_trimming
        --min_coverage $target_gene_family_assembly_cond.min_coverage
    #end if
    #if str($options_type.strand_specific) == 'yes':
        --strand_specific true
    #end if
    #if str($options_type.dereplicate) == 'yes':
        --dereplicate true
    #end if
    --min_length $options_type.min_length
#end if
--num_threads \${GALAXY_SLOTS:-4}
&& mv $output_dir/transcripts.cds '$output_cds'
&& mv $output_dir/transcripts.pep '$output_pep'
&& mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
&& mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
#if str($options_type.options_type_selector) == 'advanced':
    #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
        && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
    #end if
    #if str($options_type.dereplicate) == 'yes':
        && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
        && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
    #end if
#end if
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">
            <param name="prediction_method" type="select" label="Coding regions prediction method">