comparison funannotate_annotate.xml @ 11:9c15ca7e764e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 9e3708d04faea0f1be4ea8918e859d6f2c7eb31d

10:d0336d67702b

    --fasta '${input.fasta}'
    --species '${input.species}'
#end if

--out output

--database '$database.fields.path'

#if $sbt:
    --sbt '${sbt}'

## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:
## https://github.com/nextgenusfs/funannotate/issues/777
## The partial tbl files are combined by funannotate and are deleted below.
## The sqn files are discrete and are collected with discover_datasets.
find output/annotate_results 
-regex ".*part_[0-9]+\.\(tbl\)$"
-delete

    ]]></command>
    <inputs>

            <output_collection name="sqn" type="list">
                <element name="Genus_species">
                    <assert_contents>
                        <has_text text="Seq-submit" />
                    </assert_contents>
                </element>   
            </output_collection>
            <output name="fa_scaffolds">
                <assert_contents>
                    <has_text text=">sample" />
                </assert_contents>

            <output_collection name="sqn" type="list">
                <element name="Genus_species">
                    <assert_contents>
                        <has_text text="Seq-submit" />
                    </assert_contents>
                </element>   
            </output_collection>
            <output name="fa_scaffolds">
                <assert_contents>
                    <has_text text=">sample" />
                </assert_contents>

11:9c15ca7e764e

    --fasta '${input.fasta}'
    --species '${input.species}'
#end if

--out output
--tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"

--database '$database.fields.path'

#if $sbt:
    --sbt '${sbt}'

## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:
## https://github.com/nextgenusfs/funannotate/issues/777
## The partial tbl files are combined by funannotate and are deleted below.
## The sqn files are discrete and are collected with discover_datasets.
find output/annotate_results
-regex ".*part_[0-9]+\.\(tbl\)$"
-delete

    ]]></command>
    <inputs>

            <output_collection name="sqn" type="list">
                <element name="Genus_species">
                    <assert_contents>
                        <has_text text="Seq-submit" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="fa_scaffolds">
                <assert_contents>
                    <has_text text=">sample" />
                </assert_contents>

            <output_collection name="sqn" type="list">
                <element name="Genus_species">
                    <assert_contents>
                        <has_text text="Seq-submit" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="fa_scaffolds">
                <assert_contents>
                    <has_text text=">sample" />
                </assert_contents>