Mercurial > repos > bgruening > augustus
changeset 9:bd0e53f3a891 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4
author | iuc |
---|---|
date | Fri, 04 Oct 2024 11:32:08 +0000 |
parents | 28433faa6e42 |
children | |
files | augustus.xml macros.xml |
diffstat | 2 files changed, 60 insertions(+), 56 deletions(-) [+] |
line wrap: on
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--- a/augustus.xml Thu Aug 26 20:35:33 2021 +0000 +++ b/augustus.xml Fri Oct 04 11:32:08 2024 +0000 @@ -1,8 +1,11 @@ -<tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@"> +<tool id="augustus" name="Augustus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>gene prediction for prokaryotic and eukaryotic genomes</description> <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">augustus</xref> + </xrefs> <expand macro="requirements"/> <command detect_errors="aggressive"> <![CDATA[ @@ -97,11 +100,11 @@ </command> <inputs> <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> - <param name="noInFrameStop" argument="--noInFrameStop" type="boolean" + <param argument="--noInFrameStop" type="boolean" label="Don't report transcripts with in-frame stop codons" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur." /> - <param name="singlestrand" type="boolean" argument="--singlestrand" + <param type="boolean" argument="--singlestrand" label="Predict genes independently on each strand" help="This allows overlapping genes on opposite strands." truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> @@ -118,16 +121,17 @@ <option value="history">Run Augustus with a custom trainingset</option> </param> <when value="history"> - <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/> + <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/> </when> <when value="builtin"> - <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> + <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) --> <option value="human">Homo sapiens</option> <option value="fly">Drosophila melanogaster</option> <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option> <option value="arabidopsis">Arabidopsis thaliana</option> - <option value="brugia ">Brugia malayi</option> + <option value="brugia">Brugia malayi (brugia)</option> + <option value="brugia_malayi">Brugia malayi (brugia_malayi)</option> <option value="aedes">Aedes aegypti</option> <option value="tribolium2012">Tribolium castaneum</option> <option value="schistosoma">Schistosoma mansoni</option> @@ -136,45 +140,47 @@ <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="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="anidulans">Aspergillus nidulans (anidulans)</option> + <option value="aspergillus_nidulans">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="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="coprinus">Coprinus cinereus (coprinus)</option> + <option value="coprinus_cinereus">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="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option> + <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option> + <option value="cryptococcus">Cryptococcus neoformans (cryptococcus)</option> + <option value="cryptococcus_neoformans">Cryptococcus neoformans (cryptococcus_neoformans)</option> <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> - <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> + <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</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="histoplasma">Histoplasma capsulatum</option> - <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> - <option value="laccaria_bicolor ">Laccaria bicolor</option> + <option value="fusarium_graminearum">Fusarium graminearum</option> + <option value="histoplasma_capsulatum">Histoplasma capsulatum (histoplasma_capsulatum)</option> + <option value="histoplasma">Histoplasma capsulatum (histoplasma)</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="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="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae saccharomyces_cerevisiae_S288C</option> + <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae RM11-1a-1</option> + <option value="saccharomyces">Saccharomyces cerevisiae (saccharomyces)</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="nasonia">Nasonia vitripennis</option> <option value="tomato">Solanum lycopersicum</option> @@ -193,17 +199,12 @@ <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> <option value="wheat">Triticum aestivum</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> @@ -227,7 +228,6 @@ <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option> <option value="Aurelia_aurita">Aurelia aurita</option> <option value="Rhopilema_esculentum">Rhopilema esculentum</option> - <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option> <option value="Gonapodya_prolifera">Dunaliella salina</option> <option value="Sordaria_macrospora">Sordaria macrospora</option> <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option> @@ -250,20 +250,20 @@ </when> </conditional> - <param name="softmasking" type="boolean" argument="--softmasking" + <param type="boolean" argument="--softmasking" label="Softmasking" truevalue="1" falsevalue="0" checked="true" help="If this option is enabled, lowercase letters are considered as repeated regions." /> - <param name="strand" type="select" argument="--strand" + <param type="select" argument="--strand" label="Predict genes on specific strands"> <option value="both">both</option> <option value="forward">forward</option> <option value="backward">backward</option> </param> - <param name="genemodel" label="Gene Model" type="select" + <param argument="--genemodel" label="Gene Model" type="select" help="Gene Model to predict, for more information please refer to the help."> <option value="complete">complete</option> <option value="partial">partial</option> @@ -278,10 +278,10 @@ <option value="T">Yes</option> </param> <when value="T"> - <param name="hintsfile" label="Select hints file from history" type="data" format="gff" - help="A file containing hints in gff format (--hintsfile)"/> - <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt" - help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/> + <param argument="--hintsfile" label="Select hints file from history" type="data" format="gff" + help="A file containing hints in gff format"/> + <param name="extrinsiccfg" argument="--extrinsicCfgFile" label="Select extrinsic configuration file from history" type="data" format="txt" + help="A .cfg file listing hint sources and their boni and mali"/> </when> <when value="F"> </when> @@ -293,16 +293,16 @@ <option value="T">Yes</option> </param> <when value="T"> - <param name="start" label="Starting position" type="integer" value="" - help="The beginning of the search range (--predictionStart)"/> - <param name="stop" label="Ending position" type="integer" value="" - help="The end of the search range (--predictionEnd); must be greater than starting position"/> + <param name="start" argument="--predictionStart" label="Starting position" type="integer" value="" + help="The beginning of the search range"/> + <param name="stop" argument="--predictionEnd" label="Ending position" type="integer" value="" + help="The end of the search range; must be greater than starting position"/> </when> <when value="F"> </when> </conditional> - <param name="gff" type="boolean" label="GFF formated output" + <param name="gff" argument="--gff3" type="boolean" label="GFF formated output" help="Standard output is GTF." truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> @@ -329,14 +329,14 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> <param name="organism" value="human" /> <param name="utr" value="True" /> <param name="softmasking" value="False"/> <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/> </test> - <test> + <test expect_num_outputs="3"> <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> <param name="organism" value="human" /> <param name="utr" value="True" /> @@ -344,7 +344,7 @@ <param name="softmasking" value="False"/> <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/> </test> - <test> + <test expect_num_outputs="3"> <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> <param name="organism" value="human" /> <param name="outputs" value="protein,codingseq,introns,cds,start,stop" /> @@ -353,7 +353,7 @@ <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" /> <param name="organism" value="fly" /> <param name="usehints" value="T" /> @@ -361,6 +361,7 @@ <param name="extrinsiccfg" value="extrinsic.truncated.cfg" /> <param name="outputs" value="" /> <param name="softmasking" value="False"/> + <param name="outputs" value=""/> <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12"> <assert_contents> <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" /> @@ -369,7 +370,7 @@ </output> </test> - <test> + <test expect_num_outputs="1"> <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" /> <param name="organism" value="fly" /> <param name="usehints" value="T" /> @@ -380,6 +381,7 @@ <param name="stop" value="9000" /> <param name="outputs" value="" /> <param name="softmasking" value="False"/> + <param name="outputs" value=""/> <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12"> <assert_contents> <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" /> @@ -388,11 +390,12 @@ </output> </test> <!-- Test softmasking parameter--> - <test> + <test expect_num_outputs="1"> <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> <param name="organism" value="human" /> <param name="utr" value="True" /> <param name="softmasking" value="True"/> + <param name="outputs" value=""/> <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/> </test>
--- a/macros.xml Thu Aug 26 20:35:33 2021 +0000 +++ b/macros.xml Fri Oct 04 11:32:08 2024 +0000 @@ -2,13 +2,14 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">augustus</requirement> + <requirement type="package" version="@TOOL_VERSION@">augustus</requirement> <yield /> </requirements> </xml> - <token name="@VERSION@">3.4.0</token> - <token name="@SUFFIX_VERSION@">1</token> + <token name="@TOOL_VERSION@">3.4.0</token> + <token name="@VERSION_SUFFIX@">2</token> + <token name="@PROFILE@">23.1</token> <xml name="citations">