Mercurial > repos > iuc > data_manager_build_coreprofiler

changeset 4:45c8bfaab608 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit 7f2587b3f86c5024c7588185712d1eced9bbb037
author iuc
date Thu, 18 Dec 2025 15:21:46 +0000
parents 9e6d0309ec06
children
files data_manager/data_manager_build_coreprofiler_download.xml data_manager_conf.xml test-data/coreprofiler_scheme.loc.test tool-data/coreprofiler_scheme.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 6 files changed, 31 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_build_coreprofiler_download.xml	Fri Dec 12 21:37:42 2025 +0000
+++ b/data_manager/data_manager_build_coreprofiler_download.xml	Thu Dec 18 15:21:46 2025 +0000
@@ -2,7 +2,7 @@
     <description></description>
     <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>
@@ -124,9 +124,11 @@
     {
         "value": "coreprofiler_downloaded_${today}-${scheme_name}-${scheme_desc}-${scheme_loci}-${scheme_db}-${db_version}",
         "name": "${scheme_name}: ${scheme_desc} [${scheme_loci} loci] (${scheme_db} - ${db_date_version})",
+        "tool_version": "@TOOL_VERSION@",
+        "database": "${scheme_db}",
         "path": "coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}",
-        "database": "coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_${scheme_name}/${scheme_name}.fasta",
-        "scheme": "coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_${scheme_name}"
+        "db_path": "db_${scheme_name}/${scheme_name}.fasta",
+        "scheme_path": "scheme_${scheme_name}"
     }
     ]
 }
@@ -279,9 +281,11 @@
                     <has_text text='"coreprofiler_scheme":'/>
                     <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-borrelia_3-cgMLST-639-pubmlst-no_token"'/>
                     <has_text text='"name": "borrelia_3: cgMLST [639 loci] (pubmlst - version before 2025)"'/>
+                    <has_text_matching expression='"tool_version": "[0-9.]+"'/>
+                    <has_text_matching expression='"database": "pubmlst"'/>
                     <has_text_matching expression='"path": "coreprofiler_borrelia_3_pubmlst_no_token_[0-9-]{10}"'/>
-                    <has_text_matching expression='"database": "coreprofiler_borrelia_3_pubmlst_no_token_[0-9-]{10}/db_borrelia_3/borrelia_3.fasta"'/>
-                    <has_text_matching expression='"scheme": "coreprofiler_borrelia_3_pubmlst_no_token_[0-9-]{10}/scheme_borrelia_3"'/>
+                    <has_text text='"db_path": "db_borrelia_3/borrelia_3.fasta"'/>
+                    <has_text text='"scheme_path": "scheme_borrelia_3"'/>
                 </assert_contents>
             </output>
         </test>
@@ -297,9 +301,11 @@
                     <has_text text='"coreprofiler_scheme":'/>
                     <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-yersinia_1-Yersinia_cgMLST-500-bigsdb-no_token"'/>
                     <has_text text='"name": "yersinia_1: Yersinia_cgMLST [500 loci] (bigsdb - version before 2025)"'/>
+                    <has_text_matching expression='"tool_version": "[0-9.]+"'/>
+                    <has_text_matching expression='"database": "bigsdb"'/>
                     <has_text_matching expression='"path": "coreprofiler_yersinia_1_bigsdb_no_token_[0-9-]{10}"'/>
-                    <has_text_matching expression='"database": "coreprofiler_yersinia_1_bigsdb_no_token_[0-9-]{10}/db_yersinia_1/yersinia_1.fasta"'/>
-                    <has_text_matching expression='"scheme": "coreprofiler_yersinia_1_bigsdb_no_token_[0-9-]{10}/scheme_yersinia_1"'/>
+                    <has_text text='"db_path": "db_yersinia_1/yersinia_1.fasta"'/>
+                    <has_text text='"scheme_path": "scheme_yersinia_1"'/>
                 </assert_contents>
             </output>
         </test>
@@ -314,9 +320,11 @@
                     <has_text text='"coreprofiler_scheme":'/>
                     <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-escherichia_v1-cgMLST-2513-enterobase-no_token"'/>
                     <has_text_matching expression='"name": "escherichia_v1: cgMLST \[2513 loci\] \(enterobase - downloaded on [0-9-]{10}\)"'/>
+                    <has_text_matching expression='"tool_version": "[0-9.]+"'/>
+                    <has_text_matching expression='"database": "enterobase"'/>
                     <has_text_matching expression='"path": "coreprofiler_escherichia_v1_enterobase_no_token_[0-9-]{10}"'/>
-                    <has_text_matching expression='"database": "coreprofiler_escherichia_v1_enterobase_no_token_[0-9-]{10}/db_escherichia_v1/escherichia_v1.fasta"'/>
-                    <has_text_matching expression='"scheme": "coreprofiler_escherichia_v1_enterobase_no_token_[0-9-]{10}/scheme_escherichia_v1"'/>
+                    <has_text text='"db_path": "db_escherichia_v1/escherichia_v1.fasta"'/>
+                    <has_text text='"scheme_path": "scheme_escherichia_v1"'/>
                 </assert_contents>
             </output>
         </test>
@@ -331,9 +339,11 @@
                     <has_text text='"coreprofiler_scheme":'/>
                     <has_text_matching expression='"value": "coreprofiler_downloaded_[0-9-]{10}-mgallisepticum-Mycoplasma_gallisepticum-425-cgmlstorg-no_token"'/>
                     <has_text_matching expression='"name": "mgallisepticum: Mycoplasma_gallisepticum \[425 loci\] \(cgmlstorg - downloaded on [0-9-]{10}\)"'/>
+                    <has_text_matching expression='"tool_version": "[0-9.]+"'/>
+                    <has_text_matching expression='"database": "cgmlstorg"'/>
                     <has_text_matching expression='"path": "coreprofiler_mgallisepticum_cgmlstorg_no_token_[0-9-]{10}"'/>
-                    <has_text_matching expression='"database": "coreprofiler_mgallisepticum_cgmlstorg_no_token_[0-9-]{10}/db_mgallisepticum/mgallisepticum.fasta"'/>
-                    <has_text_matching expression='"scheme": "coreprofiler_mgallisepticum_cgmlstorg_no_token_[0-9-]{10}/scheme_mgallisepticum"'/>
+                    <has_text text='"db_path": "db_mgallisepticum/mgallisepticum.fasta"'/>
+                    <has_text text='"scheme_path": "scheme_mgallisepticum"'/>
                 </assert_contents>
             </output>
         </test>
--- a/data_manager_conf.xml	Fri Dec 12 21:37:42 2025 +0000
+++ b/data_manager_conf.xml	Thu Dec 18 15:21:46 2025 +0000
@@ -5,6 +5,8 @@
             <output> <!-- Handle the output of the Data Manager Tool -->
                 <column name="value"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="name"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="tool_version"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="database"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="path" output_ref="out_file">
                     <move type="directory">
                         <source>${path}</source>
@@ -13,8 +15,8 @@
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/coreprofiler/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
-                <column name="database"/> <!-- columns that are going to be specified by the Data Manager Tool -->
-                <column name="scheme"/> <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="db_path"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
+                <column name="scheme_path"/>  <!-- columns that are going to be specified by the Data Manager Tool -->
             </output>
         </data_table>
     </data_manager>
--- a/test-data/coreprofiler_scheme.loc.test	Fri Dec 12 21:37:42 2025 +0000
+++ b/test-data/coreprofiler_scheme.loc.test	Thu Dec 18 15:21:46 2025 +0000
@@ -4,7 +4,7 @@
 #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
\ 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
--- a/tool-data/coreprofiler_scheme.loc.sample	Fri Dec 12 21:37:42 2025 +0000
+++ b/tool-data/coreprofiler_scheme.loc.sample	Thu Dec 18 15:21:46 2025 +0000
@@ -4,7 +4,7 @@
 #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
\ 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
\ No newline at end of file
--- a/tool_data_table_conf.xml.sample	Fri Dec 12 21:37:42 2025 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Dec 18 15:21:46 2025 +0000
@@ -1,6 +1,6 @@
 <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="tool-data/coreprofiler_scheme.loc"/>
     </table>
 </tables>
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Fri Dec 12 21:37:42 2025 +0000
+++ b/tool_data_table_conf.xml.test	Thu Dec 18 15:21:46 2025 +0000
@@ -1,6 +1,6 @@
 <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.test"/>
     </table>
 </tables>
\ No newline at end of file