Mercurial > repos > genouest > braker3
changeset 3:5460380cc057 draft
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit 66b1967152f63ef95eee2058d768a5ae92502997
| author | genouest |
|---|---|
| date | Wed, 29 Nov 2023 13:35:39 +0000 |
| parents | bbe51a1c2b6b |
| children | 96ad8f880755 |
| files | braker3.xml macros.xml |
| diffstat | 2 files changed, 3 insertions(+), 11 deletions(-) [+] |
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--- a/braker3.xml Tue Oct 24 12:24:40 2023 +0000 +++ b/braker3.xml Wed Nov 29 13:35:39 2023 +0000 @@ -16,12 +16,8 @@ export PATH="\$GENEMARK_PATH/../tools/:\$PATH" && -## GeneMark only search for license in ~/.gm_key -cp '${genemark_license}' ~/.gm_key && - braker.pl --genome '${genome}' -cd $softmasking #if $evidences.bam: @@ -85,8 +81,6 @@ --useexisting ]]></command> <inputs> - <param name="genemark_license" type="data" format="txt" label="GeneMark license file" help="Braker uses GeneMark, which is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators." /> - <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should preferably be soft-masked (with RepeatMasker for example)" /> <param argument="--softmasking" type="boolean" checked="true" truevalue="" falsevalue="--softmasking_off" label="Genome sequence is soft-masked" /> @@ -132,17 +126,16 @@ </inputs> <outputs> - <data name='output_gtf' format='gtf' label="GTF Annotation" from_work_dir="braker/braker.gtf"> + <data name='output_gtf' format='gtf' label="${tool.name} on ${on_string}: GTF Annotation" from_work_dir="braker/braker.gtf"> <filter>output_format == 'gtf'</filter> </data> - <data name='output_gff' format='gff3' label="GFF Annotation" from_work_dir="braker/braker.gff3"> + <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: GFF Annotation" from_work_dir="braker/braker.gff3"> <filter>output_format == 'gff3'</filter> </data> </outputs> <tests> <test expect_failure="true"> - <param name="genemark_license" value="gm_key_64"/> <param name="genome" value="genome_masked.fa"/> <section name="evidences"> <param name="bam" value="SRR7458692.bam"/> @@ -152,7 +145,6 @@ </tests> <!-- <test expect_num_outputs="1"> - <param name="genemark_license" value="gm_key_64" /> <param name="genome" value="genome_masked.fa" /> <section name="augustus"> <param name="rounds" value="2" />