Mercurial > repos > iuc > gtdbtk_classify_wf

changeset 6:a09c8c901603 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 85683b4edaf9ec44550ff0de861023f794bf35f2
author iuc
date Fri, 13 Sep 2024 11:15:36 +0000
parents a68b985913ab
children fce109bc2aa7
files gtdbtk_classify_wf.xml macros.xml test-data/gtdbtk_database.loc test-data/gtdbtk_database_metadata_versioned.loc tool-data/gtdbtk_database.loc.sample tool-data/gtdbtk_database_metadata_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 8 files changed, 62 insertions(+), 61 deletions(-) [+]
line wrap: on
line diff
--- a/gtdbtk_classify_wf.xml	Fri Mar 08 11:35:13 2024 +0000
+++ b/gtdbtk_classify_wf.xml	Fri Sep 13 11:15:36 2024 +0000
@@ -38,7 +38,8 @@
     <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.">
-            <options from_data_table="gtdbtk_database">
+            <options from_data_table="gtdbtk_database_versioned">
+                <filter type="regexp" column="3" value="^v2(07|14)$"/>
                 <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
             </options>
         </param>
@@ -125,7 +126,7 @@
         <!-- GTDB-Tk databases are far too large to test currently -->
         <test expect_failure="true">
             <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
-            <param name="gtdbtk_db" value="gtdbtk202"/>
+            <param name="gtdbtk_db" value="gtdbtk214"/>
             <assert_stderr>
                 <has_text text="Fatal error: Exit code 1"/>
             </assert_stderr>
--- a/macros.xml	Fri Mar 08 11:35:13 2024 +0000
+++ b/macros.xml	Fri Sep 13 11:15:36 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.3.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
--- a/test-data/gtdbtk_database.loc	Fri Mar 08 11:35:13 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>  <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/
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtdbtk_database_metadata_versioned.loc	Fri Sep 13 11:15:36 2024 +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 v214	${__HERE__}/gtdbtk214/
--- a/tool-data/gtdbtk_database.loc.sample	Fri Mar 08 11:35:13 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +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>  <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/gtdbtk_database_metadata_versioned.loc.sample	Fri Sep 13 11:15:36 2024 +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/
--- a/tool_data_table_conf.xml.sample	Fri Mar 08 11:35:13 2024 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Sep 13 11:15:36 2024 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of GTDB-Tk database versions 202 and higher -->
-    <table name="gtdbtk_database" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/gtdbtk_database.loc" />
+    <table name="gtdbtk_database_versioned" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="test-data/gtdbtk_database_versioned.loc" />
     </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Fri Mar 08 11:35:13 2024 +0000
+++ b/tool_data_table_conf.xml.test	Fri Sep 13 11:15:36 2024 +0000
@@ -1,7 +1,7 @@
 <tables>
-    <!-- Location of databases for gtdbtk version 202 and higher -->
-    <table name="gtdbtk_database" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/gtdbtk_database.loc" />
+    <!-- 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" />
     </table>
 </tables>