| Previous changeset 2:e23b96d79dc0 (2022-10-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder commit 464661a59ed12a642d365f485a222764b55048a5 |
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modified:
plasmidfinder.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/plasmidfinder_database.loc tool-data/plasmidfinder_database.loc.sample |
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removed:
test-data/plasmidfinder_db.loc tool-data/plasmidfinder_db.loc.sample |
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| diff -r e23b96d79dc0 -r 7075b7a5441b plasmidfinder.xml --- a/plasmidfinder.xml Fri Oct 14 22:06:51 2022 +0000 +++ b/plasmidfinder.xml Thu Mar 02 14:58:17 2023 +0000 |
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| @@ -33,7 +33,7 @@ <section name="input" title="Input parameters" expanded="true"> <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/> <param name="database_name" type="select" label="PlasmidFinder database"> - <options from_data_table="plasmidfinder_db"> + <options from_data_table="plasmidfinder_database"> <validator message="No PlasmidFinder database is available" type="no_options"/> </options> </param> @@ -79,7 +79,7 @@ <section name="input"> <param name="input_file" value="contigs.fasta"/> <param name="input_type" value="genome"/> - <param name="database_name" value="test-plasmindfinder-db"/> + <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/> </section> <section name="output_files"> <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/> @@ -96,7 +96,7 @@ <section name="input"> <param name="input_file" value="data.fastq.gz"/> <param name="input_type" value="raw"/> - <param name="database_name" value="test-plasmindfinder-db"/> + <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/> </section> <section name="output_files"> <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/> @@ -111,7 +111,7 @@ <section name="input"> <param name="input_file" value="contigs.fasta"/> <param name="input_type" value="genome"/> - <param name="database_name" value="test-plasmindfinder-db"/> + <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/> </section> <section name="options"> <param name="min_cov" value="0.2" /> |
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| diff -r e23b96d79dc0 -r 7075b7a5441b test-data/plasmidfinder_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plasmidfinder_database.loc Thu Mar 02 14:58:17 2023 +0000 |
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| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of plasmidfinder database +# The name was obtained by merging date of download and commit number +# the columns are: +# value, name, date, path +# +# for example +plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 ${__HERE__}/test-db +plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 ${__HERE__}/test-db |
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| diff -r e23b96d79dc0 -r 7075b7a5441b test-data/plasmidfinder_db.loc --- a/test-data/plasmidfinder_db.loc Fri Oct 14 22:06:51 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -test-plasmindfinder-db Test Database ${__HERE__}/test-db |
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| diff -r e23b96d79dc0 -r 7075b7a5441b tool-data/plasmidfinder_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plasmidfinder_database.loc.sample Thu Mar 02 14:58:17 2023 +0000 |
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| @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of plasmidfinder database +# The name was obtained by merging date of download and commit number +# the columns are: +# value, name, date, path +# +# for example +#plasmidfinder_9002e7282dd0_2022-12-20 9002e7282dd0_2022-12-20 2022-12-20 plasmidfinder-db +#plasmidfinder_1307168b1ce7_2022-12-20 2.1_2022-12-20 2022-12-20 plasmidfinder-db |
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| diff -r e23b96d79dc0 -r 7075b7a5441b tool-data/plasmidfinder_db.loc.sample --- a/tool-data/plasmidfinder_db.loc.sample Fri Oct 14 22:06:51 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -#value name path -test-db-2022 "Test Database" ${__HERE__}/test-db |
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| diff -r e23b96d79dc0 -r 7075b7a5441b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Oct 14 22:06:51 2022 +0000 +++ b/tool_data_table_conf.xml.sample Thu Mar 02 14:58:17 2023 +0000 |
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| @@ -1,8 +1,8 @@ -<?xml version="1.0"?> + <tables> - <!-- Locations of plasmid database to plasmidfinder --> - <table name="plasmidfinder_db" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/plasmidfinder_db.loc" /> + <!-- Locations of plasmidfinder database in the required format --> + <table name="plasmidfinder_database" comment_char="#"> + <columns>value, name, date, path</columns> + <file path="tool-data/plasmidfinder_database.loc.sample" /> </table> </tables> |
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| diff -r e23b96d79dc0 -r 7075b7a5441b tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Fri Oct 14 22:06:51 2022 +0000 +++ b/tool_data_table_conf.xml.test Thu Mar 02 14:58:17 2023 +0000 |
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| @@ -1,8 +1,7 @@ -<?xml version="1.0"?> <tables> - <!-- Locations of plasmid database to plasmidfinder --> - <table name="plasmidfinder_db" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/plasmidfinder_db.loc" /> + <!-- Locations of plasmidfinder database in the required format --> + <table name="plasmidfinder_database" comment_char="#"> + <columns>value, name, date, path</columns> + <file path="${__HERE__}/test-data/plasmidfinder_database.loc"/> </table> </tables> |