comparison funannotate_annotate.xml @ 2:aa19eaac7d4b draft

"planemo upload commit 9cbeba115a6e13dd4c007065b7d77dcb400f72fb"

1:78407487f758

    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[

#if $uglyTestingHack == "true":
    ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
    ## Need to copy too as the test_data is read only on CI
    cp -r '${database.fields.path}' './hacked_database' &&
    sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
#end if

funannotate annotate

#if $input.input_type == 'gbk'
    --genbank '${input.genbank}'
#else

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

--out output

#if $uglyTestingHack == "true":
    --database `pwd`'/hacked_database'
#else
    --database '$database.fields.path'
#end if

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

                <filter type="sort_by" column="0" />
                <filter type="static_value" column="2" value="1.0" />
            </options>
        </param>

        <param argument="--sbt" type="data" format="sbt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />

        <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" />
        <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" />
        <param argument="--iprscan" type="data" format="xml" optional="true" label="InterProScan5 XML file" help="XML output from InterProScan" />
        <param argument="--phobius" type="data" format="tabular" optional="true" label="Phobius pre-computed results" />

            <option value="stats">Statistics</option>
            <option value="must_fix">TSV file of Gene Name/Product deflines that failed to pass tbl2asn checks and must be fixed</option>
            <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option>
            <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option>
        </param>

        <!-- Need this to change path in the test funannotate_db -->
        <param type="hidden" name="uglyTestingHack" value="" />
    </inputs>
    <outputs>
        <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">
            <filter>outputs and 'gbk' in outputs</filter>
        </data>

2:aa19eaac7d4b

    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[
funannotate annotate

#if $input.input_type == 'gbk'
    --genbank '${input.genbank}'
#else

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

--out output

--database '$database.fields.path'

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

                <filter type="sort_by" column="0" />
                <filter type="static_value" column="2" value="1.0" />
            </options>
        </param>

        <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />

        <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" />
        <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" />
        <param argument="--iprscan" type="data" format="xml" optional="true" label="InterProScan5 XML file" help="XML output from InterProScan" />
        <param argument="--phobius" type="data" format="tabular" optional="true" label="Phobius pre-computed results" />

            <option value="stats">Statistics</option>
            <option value="must_fix">TSV file of Gene Name/Product deflines that failed to pass tbl2asn checks and must be fixed</option>
            <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option>
            <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option>
        </param>
    </inputs>
    <outputs>
        <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">
            <filter>outputs and 'gbk' in outputs</filter>
        </data>