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Update gtdb-tk #6337

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merged 3 commits into from
Sep 25, 2024
Merged

Update gtdb-tk #6337

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31b02f0
fix-db-selection
paulzierep Sep 17, 2024
0d9bb1d
remove old test loc
paulzierep Sep 17, 2024
2f8cb60
bump and column name based filter
paulzierep Sep 24, 2024
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4 changes: 2 additions & 2 deletions tools/gtdbtk/gtdbtk_classify_wf.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -37,9 +37,9 @@ $advanced.force
]]></command>
<inputs>
<param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
<param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk required GTDB version R207_v2. Please contact your service administrator if this version is not available to select.">
<param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk requires GTDB version 207 or 214. Please contact your service administrator if this version is not available to select.">
<options from_data_table="gtdbtk_database_versioned">
<filter type="regexp" column="3" value="^2(07|14)$"/>
<filter type="regexp" column="version" value="^2(07|14)$"/>
<validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
</options>
</param>
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2 changes: 1 addition & 1 deletion tools/gtdbtk/macros.xml
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@@ -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>
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2 changes: 1 addition & 1 deletion ...k/test-data/gtdbtk_database_versioned.loc → ...t-data/gtdbtk_database_versioned.loc.test
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Expand Up @@ -23,4 +23,4 @@
#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/
gtdbtk214 GTDB-Tk database 214 ${__HERE__}/gtdbtk214/
3 changes: 2 additions & 1 deletion tools/gtdbtk/tool_data_table_conf.xml.test
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@@ -1,7 +1,8 @@
<?xml version="1.0"?>
<tables>
<!-- Locations of GTDB-Tk database versions 202 and higher -->
<table name="gtdbtk_database_versioned" comment_char="#">
<columns>value, name, version, path</columns>
<file path="tool-data/gtdbtk_database_versioned.loc" />
<file path="${__HERE__}/test-data/gtdbtk_database_versioned.loc.test" />
</table>
</tables>