comparison funannotate_predict.xml @ 9:d46af27fe48a draft

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

8:92c2de50f6e9

<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[

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

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

--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>

            (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) -->
        <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /-->
    </outputs>
    <tests>
        <!-- training from scratch -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="busco">
                <param name="busco_seed_species" value="fly" />
                <param name="busco_db" value="insecta" />

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- pre-trained augustus -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- bam and transcripts and proteins -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

        <!-- proteins -->
        <test>
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

9:d46af27fe48a

<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[

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

--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>

            (parameters.json file references files with absolute paths, would probably need to create an archive + edit paths in parameters.json) -->
        <!--data name='abinitio' format='json' label="${tool.name} on ${on_string}: ab-initio training parameters" from_work_dir="output/predict_results/*.parameters.json" /-->
    </outputs>
    <tests>
        <!-- training from scratch -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="busco">
                <param name="busco_seed_species" value="fly" />
                <param name="busco_db" value="insecta" />

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- pre-trained augustus -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="Found 4 preliminary alignments with diamond"/>
            </assert_stderr>
        </test>

        <!-- bam and transcripts and proteins -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>

                <has_text text="--protein_evidence"/>
            </assert_command>
        </test>

        <!-- proteins -->
        <test expect_num_outputs="10">
            <param name="input" value="genome_masked.fa" />
            <param name="database" value="2021-07-20-120000" />
            <section name="organism">
                <param name="species" value="Genus species" />
            </section>