comparison funannotate_predict.xml @ 10:1bc5a03faf2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 1102ae206f5dfb9322d28b23d224eb67a7b80a1c

9:d6c7106b7b2e

<tool id="funannotate_predict" name="Funannotate predict annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command><![CDATA[funannotate check --show-versions]]></version_command>
    <command><![CDATA[

--ploidy ${organism.ploidy}
--SeqCenter '${organism.SeqCenter}'
--SeqAccession '${organism.SeqAccession}'
--name '${organism.name}'
--numbering ${organism.numbering}

#if $parameters:
    --parameters '${parameters}'
#end if

            </conditional>
            <param argument="--weights" type="text" optional="true" label="Custom ab-initio predictor and EVM weight" help="e.g. augustus:2 pasa:10">
                <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator>
            </param>
        </section>

        <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
            <option value="gbk" selected="true">Annotated genome (genbank)</option>
            <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option>
            <option value="gff3">Annotation in GFF3 format</option>
            <option value="proteins_fa">Multi-fasta file of protein coding genes</option>

10:1bc5a03faf2e

<tool id="funannotate_predict" name="Funannotate predict annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />
    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command><![CDATA[funannotate check --show-versions]]></version_command>
    <command><![CDATA[

--ploidy ${organism.ploidy}
--SeqCenter '${organism.SeqCenter}'
--SeqAccession '${organism.SeqAccession}'
--name '${organism.name}'
--numbering ${organism.numbering}
--header_length ${header_length}

#if $parameters:
    --parameters '${parameters}'
#end if

            </conditional>
            <param argument="--weights" type="text" optional="true" label="Custom ab-initio predictor and EVM weight" help="e.g. augustus:2 pasa:10">
                <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w: ]+$</validator>
            </param>
        </section>
        <param argument="--header_length" type="integer" value="16" min="1" label="Maximum length of FASTA headers" help="The NCBI max FASTA header length is 16. Increase if you don't submit to NCBI." />
        <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
            <option value="gbk" selected="true">Annotated genome (genbank)</option>
            <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option>
            <option value="gff3">Annotation in GFF3 format</option>
            <option value="proteins_fa">Multi-fasta file of protein coding genes</option>