comparison assembly_post_processor.xml @ 66:09ae3a0d7273 draft

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65:baf10f7f3d4a

                #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}
        ]]>
    </command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
        <conditional name="prediction_method_cond">

    </inputs>
    <outputs>
        <data name="output_pttgf" format="pttgf" label="${tool.name} (targeted gene families) 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>
        <collection name="transcripts" type="list">
            <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta" />
            <param name="prediction_method" value="transdecoder" />
            <output_collection name="transcripts" type="list">
                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta" />
            <param name="prediction_method" value="estscan" />
            <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/>
            <param name="options_type_selector" value="advanced" />
            <param name="dereplicate" value="yes" />
            <output_collection name="transcripts" type="list">
                <element name="transcripts.cds" file="transcripts2.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
                <element name="transcripts.pep" file="transcripts2.pep" ftype="fasta"/>
            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
evolutionary analyses of genome-scale gene families and transcriptomes.  This tool post-processes de novo

66:09ae3a0d7273

                #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">

    </inputs>
    <outputs>
        <data name="output_pttgf" format="pttgf" label="${tool.name} (targeted gene families) on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
        </data>
        <data name="output_cds" format="fasta" label="${tool.name} on ${on_string} (transcripts.cds)"/>
        <data name="output_cleaned_cds" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.cds)"/>
        <data name="output_cleaned_nr_cds" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.nr.cds)">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
        </data>
        <data name="output_cleaned_nr_pep" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.nr.pep)">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
        </data>
        <data name="output_cleaned_pep" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.pep)"/>
        <data name="output_pep" format="fasta" label="${tool.name} on ${on_string} (transcripts.pep)"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta"/>
            <param name="prediction_method" value="transdecoder"/>
            <output name="output_cds" file="transcripts.cds" ftype="fasta"/>
            <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/>
            <output name="output_cleaned._ep" file="transcripts.cleaned.pep" ftype="fasta"/>
            <output name="output_pep" file="transcripts.pep" ftype="fasta"/>
        </test>
        <test>
            <param name="input" value="assembly.fasta" ftype="fasta"/>
            <param name="prediction_method" value="estscan"/>
            <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/>
            <param name="options_type_selector" value="advanced"/>
            <param name="dereplicate" value="yes"/>
            <output name="output_cds" file="transcripts2.cds" ftype="fasta"/>
            <output name="output_cleaned_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
            <output name="output_cleaned_nr_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
            <output name="output_cleaned_nr_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
            <output name="output_cleaned_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
            <output name="output_pep" file="transcripts2.pep" ftype="fasta"/>
        </test>
        <test>
            <param name="input" value="assembly_tgf.fasta" ftype="fasta"/>
            <param name="prediction_method" value="transdecoder"/>
            <param name="options_type_selector" value="advanced"/>
            <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"/>
            <output name="output_pep" file="transcripts_tgf.pep" ftype="fasta"/>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
evolutionary analyses of genome-scale gene families and transcriptomes.  This tool post-processes de novo