Mercurial > repos > pimarin > bakta
changeset 11:f93f54a21132 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit ed22b0f3b7b651e240154a08c9313585def1cfe5
| author | pimarin |
|---|---|
| date | Mon, 13 Feb 2023 11:37:06 +0000 |
| parents | ed4bc0577be6 |
| children | |
| files | bakta.xml test-data/TEST_1/TEST_1.embl test-data/TEST_1/TEST_1.gbff test-data/TEST_1/TEST_1.json test-data/TEST_1/TEST_1.log test-data/TEST_5/TEST_5.log tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 8 files changed, 21 insertions(+), 18 deletions(-) [+] |
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--- a/bakta.xml Mon Jan 23 16:41:16 2023 +0000 +++ b/bakta.xml Mon Feb 13 11:37:06 2023 +0000 @@ -88,7 +88,7 @@ <section name="input_option" title="Input/Output options" expanded="true"> <param name="bakta_db_select" type="select" label="The bakta database"> <options from_data_table="bakta_database"> - <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/> + <filter type="static_value" value="@BAKTA_VERSION@" column="2"/> <validator message="No bakta database is available" type="no_options"/> </options> </param> @@ -125,7 +125,7 @@ <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option> </param> <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/> - <param argument="--replicons" type="data" format="tsv,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> + <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/> <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/> </section> @@ -210,7 +210,7 @@ <section name="input_option" > <param name="bakta_db_select" value="V0.1_2022-08-29"/> <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> - <param name="input_file" value="NC_002127.1.fna"/> + <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> <param name="min_contig_length" value="250"/> </section> <section name="output_files"> @@ -238,7 +238,7 @@ <section name="input_option" > <param name="bakta_db_select" value="V0.1_2022-08-29"/> <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> - <param name="input_file" value="NC_002127.1.fna"/> + <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> <param name="min_contig_length" value="250"/> </section> <section name="organism"> @@ -274,7 +274,7 @@ <section name="input_option" > <param name="bakta_db_select" value="V0.1_2022-08-29"/> <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> - <param name="input_file" value="NC_002127.1.fna"/> + <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> <param name="min_contig_length" value="350"/> </section> <section name="workflow"> @@ -293,15 +293,15 @@ <section name="input_option" > <param name="bakta_db_select" value="V0.1_2022-08-29"/> <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> - <param name="input_file" value="NC_002127.1.fna"/> + <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> </section> <section name="annotation"> <param name="complete" value="true"/> <param name="prodigal" value="prodigal.tf"/> <param name="translation_table" value="4"/> - <param name="replicons" value="replicons.tsv"/> + <param name="replicons" value="replicons.tsv" ftype="tabular"/> <param name="compliant" value="true"/> - <param name="proteins" value="user-proteins.faa"/> + <param name="proteins" value="user-proteins.faa" ftype="fasta"/> </section> <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/> <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/> @@ -316,7 +316,7 @@ <section name="input_option" > <param name="bakta_db_select" value="V0.1_2022-08-29"/> <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> - <param name="input_file" value="NC_002127.1.fna"/> + <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> </section> <section name="annotation"> <param name="complete" value="true"/>
--- a/test-data/TEST_1/TEST_1.embl Mon Jan 23 16:41:16 2023 +0000 +++ b/test-data/TEST_1/TEST_1.embl Mon Feb 13 11:37:06 2023 +0000 @@ -14,7 +14,7 @@ CC URL: github.com/oschwengers/bakta CC CC ##Genome Annotation Summary:## -CC Annotation Date :: 01/03/2023, 10:02:08 +CC Annotation Date :: 02/10/2023, 11:57:30 CC Annotation Pipeline :: Bakta CC Annotation Software version :: v1.6.1 CC Annotation Database version :: v4.0
--- a/test-data/TEST_1/TEST_1.gbff Mon Jan 23 16:41:16 2023 +0000 +++ b/test-data/TEST_1/TEST_1.gbff Mon Feb 13 11:37:06 2023 +0000 @@ -1,4 +1,4 @@ -LOCUS contig_1 1330 bp DNA circular BCT 03-JAN-2023 +LOCUS contig_1 1330 bp DNA circular BCT 10-FEB-2023 DEFINITION plasmid unnamed1, complete sequence. ACCESSION contig_1 VERSION contig_1 @@ -13,7 +13,7 @@ URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 01/03/2023, 10:02:08 + Annotation Date :: 02/10/2023, 11:57:30 Annotation Pipeline :: Bakta Annotation Software version :: v1.6.1 Annotation Database version :: v4.0
--- a/test-data/TEST_1/TEST_1.json Mon Jan 23 16:41:16 2023 +0000 +++ b/test-data/TEST_1/TEST_1.json Mon Feb 13 11:37:06 2023 +0000 @@ -80,8 +80,8 @@ } ], "run": { - "start": "2023-01-03 10:02:07", - "end": "2023-01-03 10:02:08" + "start": "2023-02-10 11:57:29", + "end": "2023-02-10 11:57:30" }, "version": { "bakta": "1.6.1",
--- a/test-data/TEST_1/TEST_1.log Mon Jan 23 16:41:16 2023 +0000 +++ b/test-data/TEST_1/TEST_1.log Mon Feb 13 11:37:06 2023 +0000 @@ -79,7 +79,7 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/2/working +export annotation results to: /tmp/tmp3ft3p63j/job_working_directory/000/2/working human readable TSV... GFF3... INSDC GenBank & EMBL...
--- a/test-data/TEST_5/TEST_5.log Mon Jan 23 16:41:16 2023 +0000 +++ b/test-data/TEST_5/TEST_5.log Mon Feb 13 11:37:06 2023 +0000 @@ -43,7 +43,7 @@ oriCs/oriVs: 0 oriTs: 0 -export annotation results to: /tmp/tmpevwtlk9g/job_working_directory/000/14/working +export annotation results to: /tmp/tmp3ft3p63j/job_working_directory/000/14/working human readable TSV... GFF3... INSDC GenBank & EMBL...
--- a/tool_data_table_conf.xml.sample Mon Jan 23 16:41:16 2023 +0000 +++ b/tool_data_table_conf.xml.sample Mon Feb 13 11:37:06 2023 +0000 @@ -2,6 +2,10 @@ <tables> <table name="bakta_database" comment_char="#"> <columns>value, dbkey, bakta_version, path</columns> - <file path="tool-data/bakta_database.loc.sample" /> + <file path="tool-data/bakta_database.loc.sample"/> + </table> + <table name="amrfinderplus_database" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/amrfinderplus_database.loc.sample"/> </table> </tables>
--- a/tool_data_table_conf.xml.test Mon Jan 23 16:41:16 2023 +0000 +++ b/tool_data_table_conf.xml.test Mon Feb 13 11:37:06 2023 +0000 @@ -7,6 +7,5 @@ <table name="amrfinderplus_database" comment_char="#"> <columns>value, name, path</columns> <file path="${__HERE__}/test-data/amrfinderplus_database.loc" /> - </table> </tables>