Mercurial > repos > pimarin > plasmidfinder

changeset 1:c64d0c156f96 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder commit 2cb90e0f01974c35c0ea84789a3d19c704b91c84-dirty
author pimarin
date Wed, 15 Feb 2023 08:34:39 +0000
parents 7c8c8a816114
children b90300f38c54
files plasmidfinder.xml test-data/plasmidfinder_database.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 4 files changed, 7 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/plasmidfinder.xml	Tue Feb 14 16:03:07 2023 +0000
+++ b/plasmidfinder.xml	Wed Feb 15 08:34:39 2023 +0000
@@ -79,7 +79,7 @@
               <section name="input">
                   <param name="input_file" value="contigs.fasta"/>
                   <param name="input_type" value="genome"/>
-                  <param name="database_name" value="test-plasmindfinder-db"/>
+                  <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
               </section>
               <section name="output_files">
                   <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>
@@ -96,7 +96,7 @@
               <section name="input">
                   <param name="input_file" value="data.fastq.gz"/>
                   <param name="input_type" value="raw"/>
-                  <param name="database_name" value="test-plasmindfinder-db"/>
+                  <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
               </section>
               <section name="output_files">
                   <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>
@@ -111,7 +111,7 @@
               <section name="input">
                   <param name="input_file" value="contigs.fasta"/>
                   <param name="input_type" value="genome"/>
-                  <param name="database_name" value="test-plasmindfinder-db"/>
+                  <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
               </section>
               <section name="options">
                   <param name="min_cov" value="0.2" />
--- a/test-data/plasmidfinder_database.loc	Tue Feb 14 16:03:07 2023 +0000
+++ b/test-data/plasmidfinder_database.loc	Wed Feb 15 08:34:39 2023 +0000
@@ -4,5 +4,5 @@
 # value, name, date, path
 #
 # for example
-#plasmidfinder_9002e7282dd0_2022-12-20	9002e7282dd0_2022-12-20	2022-12-20	plasmidfinder-db
-#plasmidfinder_1307168b1ce7_2022-12-20	2.1_2022-12-20	2022-12-20	plasmidfinder-db
+plasmidfinder_9002e7282dd0_2022-12-20	9002e7282dd0_2022-12-20	2022-12-20	${__HERE__}/test-db
+plasmidfinder_1307168b1ce7_2022-12-20	2.1_2022-12-20	2022-12-20	${__HERE__}/test-db
--- a/tool_data_table_conf.xml.sample	Tue Feb 14 16:03:07 2023 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Feb 15 08:34:39 2023 +0000
@@ -3,6 +3,6 @@
     <!-- Locations of plasmidfinder database in the required format -->
     <table name="plasmidfinder_database" comment_char="#">
         <columns>value, name, date, path</columns>
-        <file path="tool-data/plasmidfinder.loc" />
+        <file path="tool-data/plasmidfinder_database.loc" />
     </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Tue Feb 14 16:03:07 2023 +0000
+++ b/tool_data_table_conf.xml.test	Wed Feb 15 08:34:39 2023 +0000
@@ -2,6 +2,6 @@
     <!-- Locations of plasmidfinder database in the required format -->
     <table name="plasmidfinder_database" comment_char="#">
         <columns>value, name, date,  path</columns>
-        <file path="${__HERE__}/test-data/plasmidfinder.loc.test"/>
+        <file path="${__HERE__}/test-data/plasmidfinder_database.loc"/>
     </table>
 </tables>