comparison funannotate_annotate.xml @ 8:756376aeb1ae draft

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

7:b6b5cd37f2a2

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

    --fix '${fix}'
#end if
#if $remove:
    --remove '${remove}'
#end if

--cpus \${GALAXY_SLOTS:-2}

&&

## funannotate sometimes leaves multiple *part.tbl and *part.sqn files

                    <validator type="empty_field" />
                </param>
            </when>
        </conditional>



        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />

        <param argument="--rename" type="text" label="locus_tag from NCBI to rename GFF gene models with" />
        <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID	Name	Product" />
        <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene	Product" />

        <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="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option>
            <option value="contigs_fsa">Multi-fasta file of contigs, split at gaps (use for NCBI submission)</option>
            <option value="agp">AGP file; showing linkage/location of contigs (use for NCBI submission)</option>

8:756376aeb1ae

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

    --fix '${fix}'
#end if
#if $remove:
    --remove '${remove}'
#end if
--header_length $header_length
--cpus \${GALAXY_SLOTS:-2}

&&

## funannotate sometimes leaves multiple *part.tbl and *part.sqn files

                    <validator type="empty_field" />
                </param>
            </when>
        </conditional>

        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />

        <param argument="--rename" type="text" label="locus_tag from NCBI to rename GFF gene models with" />
        <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID	Name	Product" />
        <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene	Product" />

        <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="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option>
            <option value="contigs_fsa">Multi-fasta file of contigs, split at gaps (use for NCBI submission)</option>
            <option value="agp">AGP file; showing linkage/location of contigs (use for NCBI submission)</option>