Mercurial > repos > iuc > plasmidfinder

changeset 3:7075b7a5441b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder commit 464661a59ed12a642d365f485a222764b55048a5
author iuc
date Thu, 02 Mar 2023 14:58:17 +0000
parents e23b96d79dc0
children
files plasmidfinder.xml test-data/plasmidfinder_database.loc test-data/plasmidfinder_db.loc tool-data/plasmidfinder_database.loc.sample tool-data/plasmidfinder_db.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 7 files changed, 29 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/plasmidfinder.xml	Fri Oct 14 22:06:51 2022 +0000
+++ b/plasmidfinder.xml	Thu Mar 02 14:58:17 2023 +0000
@@ -33,7 +33,7 @@
         <section name="input" title="Input parameters" expanded="true">
             <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>
             <param name="database_name" type="select" label="PlasmidFinder database">
-                <options from_data_table="plasmidfinder_db">
+                <options from_data_table="plasmidfinder_database">
                     <validator message="No PlasmidFinder database is available" type="no_options"/>
                 </options>
             </param>
@@ -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" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plasmidfinder_database.loc	Thu Mar 02 14:58:17 2023 +0000
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of plasmidfinder database
+# The name was obtained by merging date of download and commit number
+# the columns are:
+# value, name, date, path
+#
+# for example
+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/test-data/plasmidfinder_db.loc	Fri Oct 14 22:06:51 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test-plasmindfinder-db	Test Database	${__HERE__}/test-db
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/plasmidfinder_database.loc.sample	Thu Mar 02 14:58:17 2023 +0000
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of plasmidfinder database
+# The name was obtained by merging date of download and commit number
+# the columns are:
+# 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
--- a/tool-data/plasmidfinder_db.loc.sample	Fri Oct 14 22:06:51 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#value	name	path
-test-db-2022	"Test Database"  ${__HERE__}/test-db
--- a/tool_data_table_conf.xml.sample	Fri Oct 14 22:06:51 2022 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Mar 02 14:58:17 2023 +0000
@@ -1,8 +1,8 @@
-<?xml version="1.0"?>
+
 <tables>
-        <!-- Locations of plasmid database to plasmidfinder -->
-    <table name="plasmidfinder_db" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/plasmidfinder_db.loc" />
+    <!-- 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_database.loc.sample" />
     </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Fri Oct 14 22:06:51 2022 +0000
+++ b/tool_data_table_conf.xml.test	Thu Mar 02 14:58:17 2023 +0000
@@ -1,8 +1,7 @@
-<?xml version="1.0"?>
 <tables>
-        <!-- Locations of plasmid database to plasmidfinder -->
-    <table name="plasmidfinder_db" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/plasmidfinder_db.loc" />
+    <!-- Locations of plasmidfinder database in the required format -->
+    <table name="plasmidfinder_database" comment_char="#">
+        <columns>value, name, date,  path</columns>
+        <file path="${__HERE__}/test-data/plasmidfinder_database.loc"/>
     </table>
 </tables>