comparison assembly_post_processor.xml @ 80:32382b0d5add draft

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79:03716365973d

#end if
#if str($options_type.options_type_selector) == 'advanced':
    #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
    #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
        --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
        --output_pttgf '$output_pttgf'
        --output_pttgf_dir '$output_pttgf.files_path'
        --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
        --method '$target_gene_family_assembly_cond.method'
        --gap_trimming $target_gene_family_assembly_cond.gap_trimming
    #end if
    #if str($options_type.strand_specific) == 'yes':

                <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_pttgf" format="pttgf" label="Targeted gene families: ${tool.name} on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
        </data>
        <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/>
        <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/>
        <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
        </data>

            <param name="target_gene_family_assembly" value="yes"/>
            <param name="orthogroups" value="target_orthos.ids"/>
            <param name="scaffold" value="22Gv1.1"/>
            <param name="method" value="orthomcl"/>
            <param name="dereplicate" value="yes"/>
            <output name="output_pttgf" file="output.pttgf" ftype="pttgf"/>
            <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/>
            <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/>
            <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/>
            <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/>
            <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/>

80:32382b0d5add

#end if
#if str($options_type.options_type_selector) == 'advanced':
    #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
    #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
        --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 $target_gene_family_assembly_cond.gap_trimming
    #end if
    #if str($options_type.strand_specific) == 'yes':

                <param name="min_length" type="integer" value="200" label="Minimum sequence length"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <collection name="output_targeted_gene_families" type="list" label="Targeted gene families: ${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families" format="fasta" />
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
        </collection>
        <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/>
        <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/>
        <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
        </data>

            <param name="target_gene_family_assembly" value="yes"/>
            <param name="orthogroups" value="target_orthos.ids"/>
            <param name="scaffold" value="22Gv1.1"/>
            <param name="method" value="orthomcl"/>
            <param name="dereplicate" value="yes"/>
            <!--
            <output name="output_pttgf" file="output.pttgf" ftype="pttgf"/>
            -->
            <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/>
            <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/>
            <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/>
            <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/>
            <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/>