Mercurial > repos > iuc > coreprofiler_allele_calling

changeset 5:2cce87fd19ff draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler commit 7f2587b3f86c5024c7588185712d1eced9bbb037
author iuc
date Thu, 18 Dec 2025 15:21:33 +0000
parents 71693d872155
children
files coreprofiler_allele_calling.xml macro.xml test-data/coreprofiler_scheme.loc tool-data/coreprofiler_scheme.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 6 files changed, 13 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/coreprofiler_allele_calling.xml	Fri Dec 12 21:37:23 2025 +0000
+++ b/coreprofiler_allele_calling.xml	Thu Dec 18 15:21:33 2025 +0000
@@ -22,10 +22,13 @@
     #end if
 #end for
 
+#set $scheme_path = str($input_scheme.fields.path) + '/' + str($input_scheme.fields.scheme_path)
+#set $db_path = str($input_scheme.fields.path) + '/' + str($input_scheme.fields.db_path)
+
 coreprofiler allele_calling
     --query #echo ' '.join($input_files)
-    --scheme_dir '$input_scheme.fields.scheme'
-    --blast_db_path '$input_scheme.fields.database'
+    --scheme_dir '$scheme_path'
+    --blast_db_path '$db_path'
     --num_threads "\${GALAXY_SLOTS:-1}"
 
 ##Autotag
@@ -88,7 +91,7 @@
         <data name="outfa" format="fasta" label="${tool.name} on ${on_string}: Newly detected alleles" >
             <filter>scannew_section['output_selection'] and "outfa_output" in scannew_section['output_selection']</filter>
         </data>
-        <data name="num_alleles_per_locus" format="json"  label="${tool.name} on ${on_string}: Number of alleles per locus of a given scheme" >
+        <data name="num_alleles_per_locus" format="tsv"  label="${tool.name} on ${on_string}: Number of alleles per locus of a given scheme" >
             <filter>scannew_section['output_selection'] and "num_alleles_per_locus_output" in scannew_section['output_selection']</filter>
         </data>
     </outputs>
--- a/macro.xml	Fri Dec 12 21:37:23 2025 +0000
+++ b/macro.xml	Thu Dec 18 15:21:33 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.0.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="version_command">
         <version_command><![CDATA[coreprofiler --version]]></version_command>
--- a/test-data/coreprofiler_scheme.loc	Fri Dec 12 21:37:23 2025 +0000
+++ b/test-data/coreprofiler_scheme.loc	Thu Dec 18 15:21:33 2025 +0000
@@ -4,8 +4,8 @@
 #file has this format (white space characters are TAB characters)
 #
 #The columns are:
-#value	name	path	database	scheme
+#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)	coreprofiler_klebsiella_3	coreprofiler_klebsiella_3/db_klebsiella_3/klebsiella_3.fasta	coreprofiler_klebsiella_3/scheme_klebsiella_3
-coreprofiler_downloaded_20250625_klebsiella_3_scgMLST634_632_loci_bigsdb	klebsiella_3: scgMLST634 [632 loci] (BIGSdb)	${__HERE__}/coreprofiler_db	${__HERE__}/coreprofiler_db/tmp_blast_db/tmp_blast_db.fasta	${__HERE__}/coreprofiler_db/scheme_sample
\ No newline at end of file
+#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	${__HERE__}/coreprofiler_db	tmp_blast_db/tmp_blast_db.fasta	scheme_sample
\ No newline at end of file
--- a/tool-data/coreprofiler_scheme.loc.sample	Fri Dec 12 21:37:23 2025 +0000
+++ b/tool-data/coreprofiler_scheme.loc.sample	Thu Dec 18 15:21:33 2025 +0000
@@ -1,3 +1,3 @@
 #This is a sample file distributed with Galaxy that enables tools
 #file has this format (white space characters are TAB characters)
-#value	name	path	database	scheme
\ No newline at end of file
+#value	name	tool_version	database	path	db_path	scheme_path
\ No newline at end of file
--- a/tool_data_table_conf.xml.sample	Fri Dec 12 21:37:23 2025 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Dec 18 15:21:33 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
     <table name="coreprofiler_scheme" comment_char="#">
-        <columns>value, name, path, database, scheme</columns>
+        <columns>value, name, tool_version, database, path, db_path, scheme_path</columns>
         <file path="${__HERE__}/tool-data/coreprofiler_scheme.loc.sample"/>
     </table>
 </tables>
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Fri Dec 12 21:37:23 2025 +0000
+++ b/tool_data_table_conf.xml.test	Thu Dec 18 15:21:33 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tables>
     <table name="coreprofiler_scheme" comment_char="#">
-        <columns>value, name, path, database, scheme</columns>
+        <columns>value, name, tool_version, database, path, db_path, scheme_path</columns>
         <file path="${__HERE__}/test-data/coreprofiler_scheme.loc"/>
     </table>
 </tables>
\ No newline at end of file