| Previous changeset 1:f05c3732764a (2023-03-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31 |
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modified:
macros.xml pharokka.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/pharokka_db_versioned.loc tool-data/pharokka_db_versioned.loc.sample |
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removed:
test-data/pharokka_db.loc tool-data/pharokka_db.loc.sample |
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| diff -r f05c3732764a -r 2f40d2ccb0eb macros.xml --- a/macros.xml Wed Mar 22 18:05:47 2023 +0000 +++ b/macros.xml Sun Aug 06 10:12:05 2023 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.2.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">1.3.2</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="biotools"> <xrefs> @@ -33,8 +33,8 @@ </citations> </xml> <xml name="creator"> - <creator> - <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" /> - </creator> + <creator> + <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" /> + </creator> </xml> </macros> |
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| diff -r f05c3732764a -r 2f40d2ccb0eb pharokka.xml --- a/pharokka.xml Wed Mar 22 18:05:47 2023 +0000 +++ b/pharokka.xml Sun Aug 06 10:12:05 2023 +0000 |
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| @@ -1,6 +1,6 @@ <tool id="pharokka" name="pharokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> - rapid standardised annotation tool for bacteriophage genomes and metagenomes + Rapid standardised annotation tool for bacteriophage genomes and metagenomes </description> <macros> <import>macros.xml</import> @@ -43,9 +43,9 @@ </command> <inputs> <!-- the genome --> - <param type="data" name="fasta" format="fasta" help="Please upload an genome file of a bacteriophage in fasta format." label="Bacteriophage genome" /> + <param type="data" name="fasta" format="fasta" help="Please upload a genome file of a bacteriophage in fasta format." label="Bacteriophage genome" /> <param name="db_cached" type="select" label="Using built-in pharokka DB" help="Using built-in pharokka DB"> - <options from_data_table="pharokka_db"> + <options from_data_table="pharokka_db_versioned"> </options> <validator type="no_options" message="A built-in pharokka DB is not available. Please ask the galaxy admins to install one on the server." /> </param> @@ -57,7 +57,7 @@ Prodigal </option> </param> - <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="meta mode for metavirome input samples" /> + <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="Meta mode for metavirome input samples" /> <param name="evalue" type="float" value="1E-5" min="1E-20" max="10" label="E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05." /> <!-- optional arguments --> <conditional name="terminase"> |
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| diff -r f05c3732764a -r 2f40d2ccb0eb test-data/pharokka_db.loc --- a/test-data/pharokka_db.loc Wed Mar 22 18:05:47 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -pharokka_db pharokka_db Minimal DB for testing ${__HERE__}/subset_pharokka_db |
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| diff -r f05c3732764a -r 2f40d2ccb0eb test-data/pharokka_db_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pharokka_db_versioned.loc Sun Aug 06 10:12:05 2023 +0000 |
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| @@ -0,0 +1,1 @@ +pharokka_db pharokka_db v0.1 Minimal DB for testing ${__HERE__}/subset_pharokka_db |
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| diff -r f05c3732764a -r 2f40d2ccb0eb tool-data/pharokka_db.loc.sample --- a/tool-data/pharokka_db.loc.sample Wed Mar 22 18:05:47 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a pharokka DB folder. The pharokka_db.loc -#file needs this format (longer white space is the TAB character): - -#<unique_build_id> <dbkey> <display_name> <DB_folder_path> - -# for example: - -# pharokka_db pharokka_db Pharokka Database v1.2.0 /data/pharokka_db - -# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or -# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023) \ No newline at end of file |
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| diff -r f05c3732764a -r 2f40d2ccb0eb tool-data/pharokka_db_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pharokka_db_versioned.loc.sample Sun Aug 06 10:12:05 2023 +0000 |
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| @@ -0,0 +1,12 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a pharokka DB folder. The pharokka_db.loc +#file needs this format (longer white space is the TAB character): + +#<unique_build_id> <dbkey> <version> <display_name> <DB_folder_path> + +# for example: + +# pharokka_db pharokka_db v1.2.0 Pharokka Database v1.2.0 /data/pharokka_db + +# To retrieve the complete DB look at https://github.com/gbouras13/pharokka or +# use `wget "https://zenodo.org/record/7563578/files/pharokka_v1.2.0_database.tar.gz"` (14.02.2023) \ No newline at end of file |
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| diff -r f05c3732764a -r 2f40d2ccb0eb tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Mar 22 18:05:47 2023 +0000 +++ b/tool_data_table_conf.xml.sample Sun Aug 06 10:12:05 2023 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Location of pharokka DB file --> - <table name="pharokka_db" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/pharokka_db.loc" /> + <table name="pharokka_db_versioned" comment_char="#"> + <columns>value, dbkey, version, name, path</columns> + <file path="tool-data/pharokka_db_versioned.loc" /> </table> </tables> \ No newline at end of file |
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| diff -r f05c3732764a -r 2f40d2ccb0eb tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Mar 22 18:05:47 2023 +0000 +++ b/tool_data_table_conf.xml.test Sun Aug 06 10:12:05 2023 +0000 |
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| @@ -1,7 +1,7 @@ <tables> <!-- Location of pharokka DB file --> - <table name="pharokka_db" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="${__HERE__}/test-data/pharokka_db.loc" /> + <table name="pharokka_db_versioned" comment_char="#"> + <columns>value, dbkey, version, name, path</columns> + <file path="${__HERE__}/test-data/pharokka_db_versioned.loc" /> </table> </tables> \ No newline at end of file |