Mercurial > repos > iuc > coreprofiler_allele_calling

changeset 7:b781bb77a985 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler commit adc61f2c22d06e320a8a3776d5255f14ddd94e78
author iuc
date Thu, 08 Jan 2026 10:30:20 +0000
parents 49416e22e6da
children
files coreprofiler_allele_calling.xml macro.xml test-data/coreprofiler_scheme.loc test-data/coreprofiler_versioned_scheme.loc tool-data/coreprofiler_scheme.loc.sample tool-data/coreprofiler_versioned_scheme.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 8 files changed, 20 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/coreprofiler_allele_calling.xml	Thu Dec 18 15:21:57 2025 +0000
+++ b/coreprofiler_allele_calling.xml	Thu Jan 08 10:30:20 2026 +0000
@@ -63,7 +63,7 @@
     <inputs>
         <param name="input_file" type="data" format="fasta,fasta.gz" multiple="true" label="Genome assemblies in FASTA/FASTA.GZ format" help="Provide one or more genome assembly files in FASTA/FASTA.GZ format." />
         <param name="input_scheme" type="select" label="Reference allele scheme" help="Select a pre-installed reference allele scheme. If the desired scheme is not listed, please contact your Galaxy administrator.">
-            <options from_data_table="coreprofiler_scheme">
+            <options from_data_table="coreprofiler_versioned_scheme">
                 <validator message="No reference allele scheme is available" type="no_options" />
             </options>
         </param>
--- a/macro.xml	Thu Dec 18 15:21:57 2025 +0000
+++ b/macro.xml	Thu Jan 08 10:30:20 2026 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.0.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="version_command">
         <version_command><![CDATA[coreprofiler --version]]></version_command>
--- a/test-data/coreprofiler_scheme.loc	Thu Dec 18 15:21:57 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#This is a tab separated file describing the location of CoreProfiler scheme 
-#used for the CoreProfiler tool
-#
-#file has this format (white space characters are TAB characters)
-#
-#The columns are:
-#value	name	tool_version	database	path	db_path	scheme_path
-#
-#For example
-#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	1.1.1	bigsdb	coreprofiler_klebsiella_3	db_klebsiella_3/klebsiella_3.fasta	scheme_klebsiella_3
-coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	1.1.1	bigsdb	${__HERE__}/coreprofiler_db	tmp_blast_db/tmp_blast_db.fasta	scheme_sample
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coreprofiler_versioned_scheme.loc	Thu Jan 08 10:30:20 2026 +0000
@@ -0,0 +1,11 @@
+#This is a tab separated file describing the location of CoreProfiler scheme 
+#used for the CoreProfiler tool
+#
+#file has this format (white space characters are TAB characters)
+#
+#The columns are:
+#value	name	tool_version	database	path	db_path	scheme_path
+#
+#For example
+#coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	1.1.1	bigsdb	coreprofiler_klebsiella_3	db_klebsiella_3/klebsiella_3.fasta	scheme_klebsiella_3
+coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	1.1.1	bigsdb	${__HERE__}/coreprofiler_db	tmp_blast_db/tmp_blast_db.fasta	scheme_sample
\ No newline at end of file
--- a/tool-data/coreprofiler_scheme.loc.sample	Thu Dec 18 15:21:57 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#file has this format (white space characters are TAB characters)
-#value	name	tool_version	database	path	db_path	scheme_path
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/coreprofiler_versioned_scheme.loc.sample	Thu Jan 08 10:30:20 2026 +0000
@@ -0,0 +1,3 @@
+#This is a sample file distributed with Galaxy that enables tools
+#file has this format (white space characters are TAB characters)
+#value	name	tool_version	database	path	db_path	scheme_path
\ No newline at end of file
--- a/tool_data_table_conf.xml.sample	Thu Dec 18 15:21:57 2025 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Jan 08 10:30:20 2026 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
-    <table name="coreprofiler_scheme" comment_char="#">
+    <table name="coreprofiler_versioned_scheme" comment_char="#">
         <columns>value, name, tool_version, database, path, db_path, scheme_path</columns>
-        <file path="${__HERE__}/tool-data/coreprofiler_scheme.loc.sample"/>
+        <file path="${__HERE__}/tool-data/coreprofiler_versioned_scheme.loc.sample"/>
     </table>
 </tables>
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Thu Dec 18 15:21:57 2025 +0000
+++ b/tool_data_table_conf.xml.test	Thu Jan 08 10:30:20 2026 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
-    <table name="coreprofiler_scheme" comment_char="#">
+    <table name="coreprofiler_versioned_scheme" comment_char="#">
         <columns>value, name, tool_version, database, path, db_path, scheme_path</columns>
-        <file path="${__HERE__}/test-data/coreprofiler_scheme.loc"/>
+        <file path="${__HERE__}/test-data/coreprofiler_versioned_scheme.loc"/>
     </table>
 </tables>
\ No newline at end of file