Mercurial > repos > estrain > gtdbtk_classify_wf
changeset 2:bca71d3aa1bf draft default tip
planemo upload commit 21086bad5baa43e0d616b6942ded72a70840495d
| author | estrain |
|---|---|
| date | Fri, 13 Mar 2026 11:56:54 +0000 |
| parents | 353347ef2386 |
| children | |
| files | gtdbtk_classify_wf.xml test-data/gtdbtk_database_versioned.loc.test tool-data/gtdbtk_database_versioned.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 58 insertions(+), 1 deletions(-) [+] |
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--- a/gtdbtk_classify_wf.xml Thu Mar 12 20:16:30 2026 +0000 +++ b/gtdbtk_classify_wf.xml Fri Mar 13 11:56:54 2026 +0000 @@ -2,7 +2,6 @@ <description>by placement in GTDB reference tree</description> <requirements> <requirement type="package" version="2.5.2">gtdbtk</requirement> - </requirements> <command detect_errors="exit_code"><![CDATA[ #import re
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtdbtk_database_versioned.loc.test Fri Mar 13 11:56:54 2026 +0000 @@ -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/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gtdbtk_database_versioned.loc.sample Fri Mar 13 11:56:54 2026 +0000 @@ -0,0 +1,25 @@ +# 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> <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/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Mar 13 11:56:54 2026 +0000 @@ -0,0 +1,7 @@ +<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="test-data/gtdbtk_database_versioned.loc" /> + </table> +</tables> \ No newline at end of file