| Previous changeset 8:b907a3c0434f (2024-09-17) Next changeset 10:4d9445dff47b (2024-09-28) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 0f5d58e0011fcfc9c772ba9392deaed186e045eb |
|
modified:
gtdbtk_classify_wf.xml macros.xml tool_data_table_conf.xml.test |
|
added:
test-data/gtdbtk_database_versioned.loc.test |
|
removed:
test-data/gtdbtk_database_versioned.loc |
| b |
| diff -r b907a3c0434f -r 5c7ba3d85a01 gtdbtk_classify_wf.xml --- a/gtdbtk_classify_wf.xml Tue Sep 17 10:24:15 2024 +0000 +++ b/gtdbtk_classify_wf.xml Wed Sep 25 06:56:25 2024 +0000 |
| b |
| @@ -37,9 +37,9 @@ ]]></command> <inputs> <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/> - <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk required GTDB version R207_v2. Please contact your service administrator if this version is not available to select."> + <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk requires GTDB version 207 or 214. Please contact your service administrator if this version is not available to select."> <options from_data_table="gtdbtk_database_versioned"> - <filter type="regexp" column="3" value="^2(07|14)$"/> + <filter type="regexp" column="version" value="^2(07|14)$"/> <validator type="no_options" message="No locally cached GTDB-Tk database is available"/> </options> </param> |
| b |
| diff -r b907a3c0434f -r 5c7ba3d85a01 macros.xml --- a/macros.xml Tue Sep 17 10:24:15 2024 +0000 +++ b/macros.xml Wed Sep 25 06:56:25 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.3.2</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements> |
| b |
| diff -r b907a3c0434f -r 5c7ba3d85a01 test-data/gtdbtk_database_versioned.loc --- a/test-data/gtdbtk_database_versioned.loc Tue Sep 17 10:24:15 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,26 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools -# to use a directory of GTDB-Tk databases. The gtdbtk_databases.loc -# file has this format (longer white space characters are TAB characters): -# -# <unique_build_id> <display_name> <version> <directory_path> -# -# So, for example, if you have the gtdbtk 202 stored in -# /depot/data2/galaxy/gtdbtk/202/, -# then the gtdbtk_databases.loc entry would look like this: -# -# release202 gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202 -# -# and your /depot/data2/galaxy/gtdbtk/release202 directory -# would contain GTDB-Tk database files for release 202, sommething like this: -# -#drwxr-sr-x 3 gvk G-824019 4096 Apr 20 2021 fastani/ -#-rw-r--r-- 1 gvk G-824019 4810764 Apr 22 2021 manifest.tsv -#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 markers/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 masks/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 metadata/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 21 2021 mrca_red/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 msa/ -#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 pplacer/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 radii/ -#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 taxonomy/ -gtdbtk214 GTDB-Tk database v214 ${__HERE__}/gtdbtk214/ |
| b |
| diff -r b907a3c0434f -r 5c7ba3d85a01 test-data/gtdbtk_database_versioned.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtdbtk_database_versioned.loc.test Wed Sep 25 06:56:25 2024 +0000 |
| b |
| @@ -0,0 +1,26 @@ +# This is a sample file distributed with Galaxy that enables tools +# to use a directory of GTDB-Tk databases. The gtdbtk_databases.loc +# file has this format (longer white space characters are TAB characters): +# +# <unique_build_id> <display_name> <version> <directory_path> +# +# So, for example, if you have the gtdbtk 202 stored in +# /depot/data2/galaxy/gtdbtk/202/, +# then the gtdbtk_databases.loc entry would look like this: +# +# release202 gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202 +# +# and your /depot/data2/galaxy/gtdbtk/release202 directory +# would contain GTDB-Tk database files for release 202, sommething like this: +# +#drwxr-sr-x 3 gvk G-824019 4096 Apr 20 2021 fastani/ +#-rw-r--r-- 1 gvk G-824019 4810764 Apr 22 2021 manifest.tsv +#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 markers/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 masks/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 metadata/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 21 2021 mrca_red/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 msa/ +#drwxr-sr-x 4 gvk G-824019 4096 Apr 21 2021 pplacer/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 radii/ +#drwxr-sr-x 2 gvk G-824019 4096 Apr 20 2021 taxonomy/ +gtdbtk214 GTDB-Tk database 214 ${__HERE__}/gtdbtk214/ |
| b |
| diff -r b907a3c0434f -r 5c7ba3d85a01 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue Sep 17 10:24:15 2024 +0000 +++ b/tool_data_table_conf.xml.test Wed Sep 25 06:56:25 2024 +0000 |
| b |
| @@ -1,7 +1,8 @@ +<?xml version="1.0"?> <tables> <!-- Locations of GTDB-Tk database versions 202 and higher --> <table name="gtdbtk_database_versioned" comment_char="#"> <columns>value, name, version, path</columns> - <file path="tool-data/gtdbtk_database_versioned.loc" /> + <file path="${__HERE__}/test-data/gtdbtk_database_versioned.loc.test" /> </table> </tables> |