# HG changeset patch
# User iuc
# Date 1665748489 0
# Node ID eccc7495c3d911c96be30fbe04de28866d325567
# Parent  2b6e795b22a978f2c87af9441a59aedb2912c6be
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 69aab27f0210af0f0986d63575f9bfdb3f9d1f6a

diff -r 2b6e795b22a9 -r eccc7495c3d9 macro.xml
--- a/macro.xml	Mon Sep 19 08:47:42 2022 +0000
+++ b/macro.xml	Fri Oct 14 11:54:49 2022 +0000
@@ -1,7 +1,7 @@
 
 <macros>
   <token name="@TOOL_VERSION@">2.1.6</token>
-  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@VERSION_SUFFIX@">1</token>
   <token name="@PROFILE@">21.05</token>
   <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token>
 
diff -r 2b6e795b22a9 -r eccc7495c3d9 plasmidfinder.xml
--- a/plasmidfinder.xml	Mon Sep 19 08:47:42 2022 +0000
+++ b/plasmidfinder.xml	Fri Oct 14 11:54:49 2022 +0000
@@ -17,7 +17,7 @@
         -t '$options.threshold'
         #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz'
             -mp blastn
-        #else if $input.input_file.ext == 'fastqsanger.gz' or $input.input_file.ext == 'fastqsanger'
+        #elif $input.input_file.ext == 'fastqsanger' or $input.input_file.ext == 'fastqsanger.gz'
             -mp kma
         #end if
         -x
@@ -31,7 +31,7 @@
     </command>
     <inputs>
         <section name="input" title="Input parameters" expanded="true">
-            <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>
+            <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">
                     <validator message="No PlasmidFinder database is available" type="no_options"/>
@@ -39,16 +39,16 @@
             </param>
         </section>
         <section name="options" title="Options">
-            <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help="Choose a minimum coverage value (default: 0.6)"/>
-            <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help="Choose a minimum identity value (default: 0.95)"/>
+            <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help=" Fraction of matching sequence on the total target sequence(default: 0.6)"/>
+            <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help=" Fraction of shared nucleotide on the match (default: 0.95)"/>
         </section>
         <section name="output_files" title="Output file selection">
             <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
               <option value="data_json">JSON file result</option>
-              <option value="hit_fasta" selected="true">Hits in genome</option>
-              <option value="plasmid_fasta" selected="true">Plasmid hits</option>
-              <option value="result_tsv" selected="true">Plasmid results</option>
-              <option value="result_txt" selected="true">Raw results</option>
+              <option value="hit_fasta" selected="true">Matching sequences in the genome for plasmid</option>
+              <option value="plasmid_fasta" selected="true">Plasmid sequences discovered in the genome</option>
+              <option value="result_tsv" selected="true">Plasmid match list</option>
+              <option value="result_txt" selected="true">Plasmid match list in raw format</option>
               <option value="logfile">Log file</option>
             </param>
         </section>
@@ -128,20 +128,16 @@
     <help><![CDATA[
       **What it does**
       PlasmidFinder characterize plasmid sequences into whole genome sequencing.
-      It is based on [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences.
+      It is based on the [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences.
       **Input**
-      It can analyse raw data using a k-mer approach based on KMA or a blastn for genome assembly.
-      A database is need obtained from the plasmidfinder database.
-      **Options**
-      You can modify the coverage value (% of matching sequence on the total target sequence)
-      You can modify the identity threshold (% of shared nucleotide on the match)
+      PlasmidFinder takes raw data (with a k-mer analysisi) as reads or genome assembly (blastn analysis) to search plasmids.
       **Output**
       Some output files are availables
-      - A fasta file with all available hits detected in the genome
+      - A fasta file with all available sequences detected in the genome
       - A fasta file with all plasmid sequences from the database
       - A summary of the analysis in tabular format
       - A Raw result file in text format
-      - A JSON file could be use for other boinformatic analaysis
+      - A JSON file could be use for other boinformatic analysis
       - A log file with analysis parameters
 
     ]]></help>