annotate mcm_stitch.xml @ 6:4931255f2fcc draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 25b7aeca541e258a2bff5d0e34e9298996b4a47b"

<tool id="mauve-contig-mover-stitch" name="Mauve Contig Mover - Stitch" version="1.0" profile="16.04">
    <description>Concatenate multiple contigs, complementing reversed sequences and rewriting all feature coordinates</description>
    <edam_topics>
        <edam_topic>topic_0196</edam_topic>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3436</edam_operation>
        <edam_operation>operation_0232</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
        <requirement type="package" version="1.76">biopython</requirement>
    </requirements>
    <version_command><![CDATA[ $__tool_directory__/stitch.py -v ]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        python $__tool_directory__/stitch.py
        #if $seqid
            -s '$seqid'
        #else
            -s '$draft.element_identifier.replace(" ", "_")'
        #end if
        $pad_len $draft $draft.ext
        #if $contigs
            $contigs
        #end if
        > $output
    ]]></command>
    <inputs>
        <param name="draft" type="data" format="abi,abi-trim,ace,cif-atom,cif-seqres,clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,ig,imgt,nexus,pdb-seqres,pdb-atom,phd,phylip,pir,seqxml,sff,sff-trim,stockholm,swiss,tab,qual,uniprot-xml,gff3" label="Draft" />
        <param name="contigs" type="data" format="tabular" label="Contigs" optional="true" help="Contigs output from Mauve Contig Mover" />
        <param name="pad_len" type="integer" min="0" value="1000" label="Pad length" help="Specify the length of padding to put between contigs" />
        <param name="seqid" type="text" value="" label="Stitched sequence ID" help="Specify an ID to use for the stitched record, the dataset ID is used otherwise" />
    </inputs>
    <outputs>
        <data name="output" format_source="draft" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="draft" value="test-data/draft_bioperl.gbff" ftype="genbank" />
            <param name="contigs" value="test-data/contig_order.tabular" ftype="tabular" />
            <output name="output" checksum="sha256:08afe06a0f1eb96aa7f2a5b9e8a5ca15a4775c884f3144b6d82f2a0668cdb210" ftype="genbank" />
        </test>
    </tests>
    <help><![CDATA[
        Stitch contigs into a single contig.
        Compliments reversed sequences and rewrites all feature coordinates.
        For gankbank and embl, 'source' features are combined.
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.3364789</citation>
    </citations>
</tool>