comparison maker.xml @ 9:a444254e9a57 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 739da8be15072cfd98cc0b8d6bfa9dedb25a98f0"

8:3c1a01127868

<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_VERSION@">
    <description>genome annotation pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
        RM_PATH=\$(which RepeatMasker) &&
        if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&

TMP= # specify a directory other than the system default temporary directory for temporary files
        ]]></configfile>
    </configfiles>

    <inputs>
        <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
        <param name="organism_type" type="select" label="Organism type">
            <option value="eukaryotic">Eukaryotic</option>
            <option value="prokaryotic">Prokaryotic</option>
        </param>

                    <param name="augustus_species" type="select" label="Augustus species model">
                        <!-- If you update this list, please also update it in augustus and busco tools (../augustus/augustus.xml and ../busco/busco.xml) -->
                        <option value="human">Homo sapiens</option>
                        <option value="fly">Drosophila melanogaster</option>
                        <option value="arabidopsis">Arabidopsis thaliana</option>
                        <option value="brugia ">Brugia malayi</option>
                        <option value="aedes">Aedes aegypti</option>
                        <option value="tribolium2012">Tribolium castaneum</option>
                        <option value="schistosoma">Schistosoma mansoni</option>
                        <option value="tetrahymena">Tetrahymena thermophila</option>
                        <option value="galdieria">Galdieria sulphuraria</option>
                        <option value="maize">Zea mays</option>
                        <option value="toxoplasma">Toxoplasma gondii</option>
                        <option value="caenorhabditis ">Caenorhabditis elegans</option>
                        <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
                        <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
                        <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
                        <option value="aspergillus_terreus">Aspergillus terreus</option>
                        <option value="botrytis_cinerea ">Botrytis cinerea</option>
                        <option value="candida_albicans ">Candida albicans</option>
                        <option value="candida_guilliermondii ">Candida guilliermondii</option>
                        <option value="candida_tropicalis ">Candida tropicalis</option>
                        <option value="chaetomium_globosum">Chaetomium globosum</option>
                        <option value="coccidioides_immitis">Coccidioides immitis</option>
                        <option value="coprinus">Coprinus cinereus</option>
                        <option value="coprinus_cinereus">Coprinus cinereus</option>
                        <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
                        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
                        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
                        <option value="cryptococcus">Cryptococcus neoformans</option>
                        <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
                        <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
                        <option value="eremothecium_gossypii">Eremothecium gossypii</option>
                        <option value="fusarium_graminearum ">Fusarium graminearum</option>
                        <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
                        <option value="histoplasma">Histoplasma capsulatum</option>
                        <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
                        <option value="laccaria_bicolor ">Laccaria bicolor</option>
                        <option value="lamprey">Petromyzon marinus</option>
                        <option value="leishmania_tarentolae">Leishmania tarentolae</option>
                        <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
                        <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
                        <option value="neurospora_crassa">Neurospora crassa</option>
                        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                        <option value="pichia_stipitis">Pichia stipitis</option>
                        <option value="rhizopus_oryzae">Rhizopus oryzae</option>
                        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
                        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
                        <option value="saccharomyces">Saccharomyces cerevisiae</option>
                        <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
                        <option value="trichinella">Trichinella spiralis</option>
                        <option value="ustilago_maydis">Ustilago maydis</option>
                        <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>

                        <option value="coyote_tobacco">Coyote tobacco</option>
                        <option value="s_aureus">Staphylococcus aureus</option>
                        <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
                        <option value="wheat">wheat</option>
                        <option value="zebrafish">Danio rerio</option>
                        <option value="anidulans">Aspergillus nidulans</option>
                        <option value="bombus_impatiens1">Bombus impatiens1</option>
                        <option value="bombus_terrestris2">Bombus terrestris2</option>
                        <option value="botrytis_cinerea">Botrytis cinerea</option>
                        <option value="brugia_malayi">Brugia malayi</option>
                        <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
                        <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
                        <option value="culex_pipiens">Culex pipiens</option>
                        <option value="elephant_shark">Callorhinchus milii</option>
                        <option value="honeybee1">Apis mellifera</option>
                        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                        <option value="pea_aphid">Acyrthosiphon pisum</option>
                        <option value="rhodnius_prolixus">Rhodnius prolixus</option>
                        <option value="ustilago_maydis">Ustilago maydis</option>
                        <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
                        <option value="verticillium_longisporum1">Verticillium longisporum1</option>
                        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
                        <option value="adorsata">adorsata</option>
                        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
                        <option value="maker2_athal1">maker2_athal1</option>
                        <option value="maker2_c_elegans1">maker2_c_elegans1</option>
                        <option value="maker2_dmel1">maker2_dmel1</option>
                        <option value="maker2_spomb1">maker2_spomb1</option>
                        <option value="parasteatoda">parasteatoda</option>

        <data format="gff3" name="output_evidences" label="${tool.name} on ${on_string}: evidences"/>
        <data format="gff3" name="output_full" label="${tool.name} on ${on_string}: full gff (evidences + final annotation)"/>
    </outputs>
    <tests>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot.gff3"/>
            <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="organism_type" value="prokaryotic"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_proc.gff3"/>
            <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="reannotation|reannotate" value="yes"/>
            <param name="reannotation|maker_gff" value="evidences.gff3"/>
            <param name="reannotation|est_pass" value="true"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_reuse.gff3"/>
            <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="builtin"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_species" value="human"/>
            <param name="est_evidences|est" value="est.fasta"/>

            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>
            <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="history"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
            <param name="est_evidences|est" value="est.fasta"/>

            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>
            <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_norm.gff3"/>
            <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="dfam"/>
            <param name="repeat_masking|repeat_source|species_list" value="drosophila" />
            <output name="output_gff" file="annot_dfam.gff3"/>
            <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="dfam_up"/>
            <param name="repeat_masking|repeat_source|dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />
            <param name="repeat_masking|repeat_source|species_name" value="rodent" />
            <output name="output_gff" file="annot_dfam_up.gff3"/>
            <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="non_IUPAC.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <param name="advanced|fix_nucleotides" value="true"/>

9:a444254e9a57

<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_VERSION@">
    <description>genome annotation pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">maker</xref>
    </xrefs>
    <expand macro="requirements"/>
    <command><![CDATA[
        RM_PATH=\$(which RepeatMasker) &&
        if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&

TMP= # specify a directory other than the system default temporary directory for temporary files
        ]]></configfile>
    </configfiles>

    <inputs>
        <!-- More info on licensing in https://github.com/galaxyproject/iwc/pull/47#issuecomment-962260646 -->
        <param name="license_agreement" type="boolean" label="Are you running Maker for academic use, or did you purchase a license?"
            help="The MAKER authors specifically allowed to make it available on Galaxy. MAKER is free for academic use, but commercial Galaxy users of MAKER still need a license, which can be obtained at http://weatherby.genetics.utah.edu/cgi-bin/registration/maker_license.cgi">
            <validator type="expression" message="You must either run Maker for academic use, or purchase a license.">value</validator>
        </param>

        <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
        <param name="organism_type" type="select" label="Organism type">
            <option value="eukaryotic">Eukaryotic</option>
            <option value="prokaryotic">Prokaryotic</option>
        </param>

                    <param name="augustus_species" type="select" label="Augustus species model">
                        <!-- If you update this list, please also update it in augustus and busco tools (../augustus/augustus.xml and ../busco/busco.xml) -->
                        <option value="human">Homo sapiens</option>
                        <option value="fly">Drosophila melanogaster</option>
                        <option value="arabidopsis">Arabidopsis thaliana</option>
                        <option value="aedes">Aedes aegypti</option>
                        <option value="tribolium2012">Tribolium castaneum</option>
                        <option value="schistosoma">Schistosoma mansoni</option>
                        <option value="tetrahymena">Tetrahymena thermophila</option>
                        <option value="galdieria">Galdieria sulphuraria</option>
                        <option value="maize">Zea mays</option>
                        <option value="toxoplasma">Toxoplasma gondii</option>
                        <option value="caenorhabditis">Caenorhabditis elegans</option>
                        <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
                        <option value="aspergillus_nidulans">Aspergillus nidulans</option>
                        <option value="aspergillus_oryzae">Aspergillus oryzae</option>
                        <option value="aspergillus_terreus">Aspergillus terreus</option>
                        <option value="botrytis_cinerea">Botrytis cinerea</option>
                        <option value="candida_albicans">Candida albicans</option>
                        <option value="candida_guilliermondii">Candida guilliermondii</option>
                        <option value="candida_tropicalis">Candida tropicalis</option>
                        <option value="chaetomium_globosum">Chaetomium globosum</option>
                        <option value="coccidioides_immitis">Coccidioides immitis</option>
                        <option value="coprinus_cinereus">Coprinus cinereus</option>
                        <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
                        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
                        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
                        <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
                        <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
                        <option value="eremothecium_gossypii">Eremothecium gossypii</option>
                        <option value="fusarium_graminearum">Fusarium graminearum</option>
                        <option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
                        <option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
                        <option value="laccaria_bicolor">Laccaria bicolor</option>
                        <option value="lamprey">Petromyzon marinus</option>
                        <option value="leishmania_tarentolae">Leishmania tarentolae</option>
                        <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
                        <option value="magnaporthe_grisea">Magnaporthe grisea</option>
                        <option value="neurospora_crassa">Neurospora crassa</option>
                        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
                        <option value="pichia_stipitis">Pichia stipitis</option>
                        <option value="rhizopus_oryzae">Rhizopus oryzae</option>
                        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
                        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a_1</option>
                        <option value="saccharomyces">Saccharomyces cerevisiae</option>
                        <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
                        <option value="trichinella">Trichinella spiralis</option>
                        <option value="ustilago_maydis">Ustilago maydis</option>
                        <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>

                        <option value="coyote_tobacco">Coyote tobacco</option>
                        <option value="s_aureus">Staphylococcus aureus</option>
                        <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
                        <option value="wheat">wheat</option>
                        <option value="zebrafish">Danio rerio</option>
                        <option value="bombus_impatiens1">Bombus impatiens1</option>
                        <option value="bombus_terrestris2">Bombus terrestris2</option>
                        <option value="brugia_malayi">Brugia malayi</option>
                        <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
                        <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
                        <option value="culex_pipiens">Culex pipiens</option>
                        <option value="elephant_shark">Callorhinchus milii</option>
                        <option value="honeybee1">Apis mellifera</option>
                        <option value="pea_aphid">Acyrthosiphon pisum</option>
                        <option value="rhodnius_prolixus">Rhodnius prolixus</option>
                        <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
                        <option value="verticillium_longisporum1">Verticillium longisporum1</option>
                        <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
                        <option value="adorsata">adorsata</option>
                        <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
                        <option value="maker2_athal1">maker2_athal1</option>
                        <option value="maker2_c_elegans1">maker2_c_elegans1</option>
                        <option value="maker2_dmel1">maker2_dmel1</option>
                        <option value="maker2_spomb1">maker2_spomb1</option>
                        <option value="parasteatoda">parasteatoda</option>

        <data format="gff3" name="output_evidences" label="${tool.name} on ${on_string}: evidences"/>
        <data format="gff3" name="output_full" label="${tool.name} on ${on_string}: full gff (evidences + final annotation)"/>
    </outputs>
    <tests>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot.gff3"/>
            <output name="output_evidences" file="evidences.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="organism_type" value="prokaryotic"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_proc.gff3"/>
            <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="reannotation|reannotate" value="yes"/>
            <param name="reannotation|maker_gff" value="evidences.gff3"/>
            <param name="reannotation|est_pass" value="true"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_reuse.gff3"/>
            <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="builtin"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_species" value="human"/>
            <param name="est_evidences|est" value="est.fasta"/>

            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>
            <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="abinitio_gene_prediction|snaphmm" value="snap.hmm"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_mode" value="history"/>
            <param name="abinitio_gene_prediction|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
            <param name="est_evidences|est" value="est.fasta"/>

            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>
            <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <output name="output_gff" file="annot_norm.gff3"/>
            <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="dfam"/>
            <param name="repeat_masking|repeat_source|species_list" value="drosophila" />
            <output name="output_gff" file="annot_dfam.gff3"/>
            <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="est.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="dfam_up"/>
            <param name="repeat_masking|repeat_source|dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />
            <param name="repeat_masking|repeat_source|species_name" value="rodent" />
            <output name="output_gff" file="annot_dfam_up.gff3"/>
            <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
        </test>
        <test>
            <param name="license_agreement" value="true" />
            <param name="genome" value="genome.fasta"/>
            <param name="est_evidences|est" value="non_IUPAC.fasta"/>
            <param name="est_evidences|est2genome" value="1"/>
            <param name="repeat_masking|repeat_source|source_type" value="no"/>
            <param name="advanced|fix_nucleotides" value="true"/>