comparison funannotate_predict.xml @ 13:3e13e35ef26b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

12:4b96ced19f75

#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

mkdir -p input/ &&
ln -s '${input}' input/input.fasta &&

funannotate predict
--input input/input.fasta
--out output
--tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
#if $uglyTestingHack == "true":
    --database `pwd`'/hacked_database'
#else
    --database '$database.fields.path'
#end if

$force

--species '${organism.species}'
--isolate '${organism.isolate}'

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

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

#if $evidences.rna_bam
    --rna_bam ${evidences.rna_bam}
#end if

--p2g_prefilter ${evidences.p2g_prefilter}

--busco_seed_species '${busco.busco_seed_species}'
--busco_db '${busco.busco_db}'

#if $augustus.augustus_species != 'none':
    --augustus_species '${augustus.augustus_species}'
#end if
--min_training_models ${augustus.min_training_models}
${augustus.optimize_augustus}

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

        <param argument="--force" type="boolean" checked="true" truevalue="" falsevalue="--force" label="Check the genome sequence" help="Disable at your own risk if you want to ignore problems in the genome sequence reported by Funannotate" />

        <section name="busco" expanded="true" title="Busco">
            <param argument="--busco_db" type="select" label="BUSCO models to align" help="BUSCO will be used to perform initial training of ab initio predictors (e.g. Augustus).">
                <expand macro="busco_species"/>
            </param>
            <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally.">
                <expand macro="augustus_species"/>
            </param>
        </section>

        <section name="filtering" expanded="true" title="Filtering">
            <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" />
            <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" />
            <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" />
            <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />
            <param argument="--repeat_filter" type="select" label="Repetitive gene model filtering" help="'overlap' drops gene models that are more than 90% contained within a repeat region; 'blast' compares the amino acid sequences to a small database of known transposons">
                <option value="overlap blast" selected="True">overlap + blast</option>
                <option value="overlap">overlap</option>
                <option value="blast">blast</option>
                <option value="none">none</option>
            </param>
        </section>

        <param argument="--parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." />

        <section name="augustus" expanded="false" title="Augustus settings (advanced)">
            <param argument="--augustus_species" type="select" label="Augustus species training set" help="Select a species from the list">
                <option value="none" selected="True">No corresponding species, train from scratch</option>
                <expand macro="augustus_species"/>
            </param>
            <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" />
            <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" />
        </section>

13:3e13e35ef26b

#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' &&
    #set db_path='$(pwd)/hacked_database'
#else
    #set db_path=$database.fields.path
#end if

## show detailed info about the reference DB on stdout
export FUNANNOTATE_DB="$db_path" &&
funannotate database &&

mkdir -p input/ &&
ln -s '${input}' input/input.fasta &&

funannotate predict
--input input/input.fasta
--out output
--tmpdir "\${_GALAXY_JOB_TMP_DIR:-/tmp}"
--database "$db_path"

$force

--species '${organism.species}'
--isolate '${organism.isolate}'

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

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

#if $evidences.rna_bam
    --rna_bam ${evidences.rna_bam}
#end if

--p2g_prefilter ${evidences.p2g_prefilter}

--busco_seed_species '${busco.busco_seed_species}'
--busco_db '${busco.busco_db}'

#if $augustus.augustus_species:
    --augustus_species '${augustus.augustus_species}'
#end if
--min_training_models ${augustus.min_training_models}
${augustus.optimize_augustus}

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

        <param argument="--force" type="boolean" checked="true" truevalue="" falsevalue="--force" label="Check the genome sequence" help="Disable at your own risk if you want to ignore problems in the genome sequence reported by Funannotate" />

        <section name="busco" expanded="true" title="Busco">
            <param argument="--busco_db" type="select" label="BUSCO models to align" help="BUSCO will be used to perform initial training of ab initio predictors (e.g. Augustus).">
                <expand macro="busco_species"/>
            </param>
            <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally.">
                <expand macro="busco_seeds">
                    <filter type="add_value" value="anidulans" name="Anidulans" index="0"/> <!-- this sets the default -->
                </expand>
            </param>
        </section>

        <section name="filtering" expanded="true" title="Filtering">
            <param argument="--min_intronlen" type="integer" value="10" min="0" label="Minimum intron length" />
            <param argument="--max_intronlen" type="integer" value="3000" min="0"  label="Maximum intron length" />
            <param argument="--min_protlen" type="integer" value="50" min="0" label="Minimum protein length" />
            <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />
            <param argument="--repeat_filter" type="select" label="Repetitive gene model filtering" help="'overlap' drops gene models that are more than 90% contained within a repeat region; 'blast' compares the amino acid sequences to a small database of known transposons">
                <option value="overlap blast" selected="True">overlap + blast</option>
                <option value="overlap">overlap</option>
                <option value="blast">blast</option>
                <option value="none">none</option>
            </param>
        </section>

        <!-- <param argument="\-\-parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." /> -->

        <section name="augustus" expanded="false" title="Augustus settings (advanced)">
            <param argument="--augustus_species" type="select" optional="true" label="Augustus species training set" help="Select a species from the list, use species name if empty">
                <expand macro="busco_seeds"/>
            </param>
            <param argument="--min_training_models" type="integer" value="200" label="Minimum number of models to train Augustus" />
            <param argument="--optimize_augustus" type="boolean" checked="false" truevalue="--optimize_augustus" falsevalue="" label="Run 'optimize_augustus.pl' to refine training (long runtime)" />
        </section>