| Previous changeset 8:28433faa6e42 (2021-08-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit fbd55928544683a7f7e6e10dadabe698bc71b0e4 |
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modified:
augustus.xml macros.xml |
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| diff -r 28433faa6e42 -r bd0e53f3a891 augustus.xml --- a/augustus.xml Thu Aug 26 20:35:33 2021 +0000 +++ b/augustus.xml Fri Oct 04 11:32:08 2024 +0000 |
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| b'@@ -1,8 +1,11 @@\n-<tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@">\n+<tool id="augustus" name="Augustus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>gene prediction for prokaryotic and eukaryotic genomes</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">augustus</xref>\n+ </xrefs>\n <expand macro="requirements"/>\n <command detect_errors="aggressive">\n <![CDATA[\n@@ -97,11 +100,11 @@\n </command>\n <inputs>\n <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>\n- <param name="noInFrameStop" argument="--noInFrameStop" type="boolean"\n+ <param argument="--noInFrameStop" type="boolean"\n label="Don\'t report transcripts with in-frame stop codons"\n truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"\n help="Otherwise, intron-spanning stop codons could occur." />\n- <param name="singlestrand" type="boolean" argument="--singlestrand"\n+ <param type="boolean" argument="--singlestrand"\n label="Predict genes independently on each strand"\n help="This allows overlapping genes on opposite strands."\n truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />\n@@ -118,16 +121,17 @@\n <option value="history">Run Augustus with a custom trainingset</option>\n </param>\n <when value="history">\n- <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the \'Train Augustus\' tool"/>\n+ <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the \'Train Augustus\' tool"/>\n </when>\n <when value="builtin">\n- <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">\n+ <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">\n <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->\n <option value="human">Homo sapiens</option>\n <option value="fly">Drosophila melanogaster</option>\n <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option>\n <option value="arabidopsis">Arabidopsis thaliana</option>\n- <option value="brugia ">Brugia malayi</option>\n+ <option value="brugia">Brugia malayi (brugia)</option>\n+ <option value="brugia_malayi">Brugia malayi (brugia_malayi)</option>\n <option value="aedes">Aedes aegypti</option>\n <option value="tribolium2012">Tribolium castaneum</option>\n <option value="schistosoma">Schistosoma mansoni</option>\n@@ -136,45 +140,47 @@\n <option value="galdieria">Galdieria sulphuraria</option>\n <option value="maize">Zea mays</option>\n <option value="toxoplasma">Toxoplasma gondii</option>\n- <option value="caenorhabditis ">Caenorhabditis elegans</option>\n+ <option value="caenorhabditis">Caenorhabditis elegans</option>\n <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>\n- <option value="aspergillus_nidulans ">Aspergillus nidulans</option>\n- <option value="aspergillus_oryzae ">Aspergillus oryzae</option>\n+ <option value="anidulans">Aspergillus nidulans (anidulans)</option>\n+ <'..b'e search range; must be greater than starting position"/>\n </when>\n <when value="F">\n </when>\n </conditional>\n \n- <param name="gff" type="boolean" label="GFF formated output"\n+ <param name="gff" argument="--gff3" type="boolean" label="GFF formated output"\n help="Standard output is GTF."\n truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />\n \n@@ -329,14 +329,14 @@\n </data>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="3">\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n <param name="utr" value="True" />\n <param name="softmasking" value="False"/>\n <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>\n </test>\n- <test>\n+ <test expect_num_outputs="3">\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n <param name="utr" value="True" />\n@@ -344,7 +344,7 @@\n <param name="softmasking" value="False"/>\n <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>\n </test>\n- <test>\n+ <test expect_num_outputs="3">\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />\n@@ -353,7 +353,7 @@\n <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />\n <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />\n <param name="organism" value="fly" />\n <param name="usehints" value="T" />\n@@ -361,6 +361,7 @@\n <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />\n <param name="outputs" value="" />\n <param name="softmasking" value="False"/>\n+ <param name="outputs" value=""/>\n <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">\n <assert_contents>\n <has_text_matching expression="chr2R\\tAUGUSTUS\\tgene\\t7560\\t9303\\t0\\.(7[8-9]|8[0-5])\\t-\\t.\\tchr2R.g1" />\n@@ -369,7 +370,7 @@\n </output>\n \n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />\n <param name="organism" value="fly" />\n <param name="usehints" value="T" />\n@@ -380,6 +381,7 @@\n <param name="stop" value="9000" />\n <param name="outputs" value="" />\n <param name="softmasking" value="False"/>\n+ <param name="outputs" value=""/>\n <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">\n <assert_contents>\n <has_text_matching expression="chr2R\\tAUGUSTUS\\tgene\\t7560\\t8931\\t0.8[2-5]\\t-\\t.\\tchr2R.g1" />\n@@ -388,11 +390,12 @@\n </output>\n </test>\n <!-- Test softmasking parameter-->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n <param name="organism" value="human" />\n <param name="utr" value="True" />\n <param name="softmasking" value="True"/>\n+ <param name="outputs" value=""/>\n <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>\n </test>\n \n' |
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| diff -r 28433faa6e42 -r bd0e53f3a891 macros.xml --- a/macros.xml Thu Aug 26 20:35:33 2021 +0000 +++ b/macros.xml Fri Oct 04 11:32:08 2024 +0000 |
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| @@ -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"> |