annotate gff3_extract_sequence.xml @ 10:3d9f283ff09d draft default tip

planemo upload commit e14699677f337fd1324aa6898c1388796c5446c1-dirty

<tool id="edu.tamu.cpt.gff3.export_seq" name="GFF3 Feature Sequence Export" version="19.1.0.0">
    <description>Export corresponding sequence in genome from GFF3</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
        @GENOME_SELECTOR_PRE@

        '$__tool_directory__/gff3_extract_sequence.py'

        @GENOME_SELECTOR@

        @INPUT_GFF@

        #if $feature_filter and $feature_filter is not None:
        --feature_filter $feature_filter
        #end if
        #if $nodesc
            --nodesc
        #end if
        > '$default']]>
    </command>
    <inputs>
        <expand macro="genome_selector"/>
        <expand macro="gff3_input"/>
        <param label="Filter for specific feature types" name="feature_filter" type="text" help="Use 'nice_cds' if your features are coming from Apollo, however this will fail on non-Apollo data"/>
        <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/>
    </inputs>
    <outputs>
        <data format="fasta" hidden="false" name="default"/>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="T7_ExtSeqIn.fasta"/>
            <param name="gff3_data" value="T7_ExtSeqIn.gff3"/>
            <param name="nodesc" value=""/>
            <param name="feature_filter" value="CDS"/>
            <output name="output" file="T7_ExtSeqOut.fasta"/>
        </test>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="Miro_ExtSeqIn.fa"/>
            <param name="gff3_data" value="Miro_ExtSeqIn.gff3"/>
            <param name="nodesc" value=""/>
            <param name="feature_filter" value="CDS"/>
            <output name="output" file="Miro_ExtSeqOut1.fa"/>
        </test>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="Miro_ExtSeqIn.fa"/>
            <param name="gff3_data" value="Miro_ExtSeqIn.gff3"/>
            <param name="feature_filter" value="CDS"/>
            <param name="nodesc" value="--nodesc"/>
            <output name="output" file="Miro_ExtSeqOut2.fa"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

From the FASTA sequence for a genome, extracts the *nucleotide* sequences for 
all CDSs in an input GFF3 and outputs them as a multi-FASTA formatted file.

The filter for specific feature types was designed for data retrieved from Apollo. 
Using ‘unique_cds’ extracts the sequence for all CDS. Using ‘nice_cds’ will extract 
the sequence only for CDS features with a start codon (recommended). If a gene from
Apollo has multiple CDSs, the tool will append a "_##" to the end of subsequent genes.

      ]]></help>
    <expand macro="citations"/>
</tool>