--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plasmidfinder.xml	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,149 @@
+<tool id="plasmidfinder" name="PlasmidFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Plasmid identification in bacteria.
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        mkdir output_dir &&
+        mkdir temp_dir &&
+        plasmidfinder.py
+        -i '$input.input_file'
+        -p '$input.database_name.fields.path'
+        -l '$options.min_cov'
+        -t '$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 $input.input_file.ext == 'fastqsanger'
+            -mp kma
+        #end if
+        -x
+        -o output_dir
+        -tmp temp_dir
+        #*======================================
+                            LOG file
+        ======================================*#
+        | tee '$log_file'
+        ]]>
+    </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="database_name" type="select" label="PlasmidFinder database">
+                <options from_data_table="plasmidfinder_db">
+                    <validator message="No PlasmidFinder database is available" type="no_options"/>
+                </options>
+            </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)"/>
+        </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="logfile">Log file</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="json_file" format="json" from_work_dir="output_dir/data.json" label="${tool.name} on ${on_string}: data.json">
+            <filter>  "data_json" in output_files['output_selection'] </filter>
+        </data>
+        <data name="hit_file" format="fasta" from_work_dir="output_dir/Hit_in_genome_seq.fsa" label="${tool.name} on ${on_string}: hit_in_genome.fasta">
+            <filter>  "hit_fasta" in output_files['output_selection'] </filter>
+        </data>
+        <data name="plasmid_file" format="fasta" from_work_dir="output_dir/Plasmid_seqs.fsa" label="${tool.name} on ${on_string}: plasmid.fasta">
+            <filter> "plasmid_fasta" in output_files['output_selection'] </filter>
+        </data>
+        <data name="result_file" format="tabular" from_work_dir="output_dir/results_tab.tsv" label="${tool.name} on ${on_string}: results.tsv">
+            <filter>  "result_tsv" in output_files['output_selection'] </filter>
+        </data>
+        <data name="raw_file" format="txt" from_work_dir="output_dir/results.txt" label="${tool.name} on ${on_string}: raw_result.txt">
+            <filter>  "result_txt" in output_files['output_selection'] </filter>
+        </data>
+        <data name="log_file" format="txt" from_work_dir="output_dir" label="${tool.name} on ${on_string}: log file">
+            <filter>  "logfile" in output_files['output_selection'] </filter>
+        </data>
+    </outputs>
+    <tests>
+        <!--test_1 with default value and all output files for contigs -->
+        <test expect_num_outputs="6">
+              <section name="input">
+                  <param name="input_file" value="contigs.fasta"/>
+                  <param name="input_type" value="genome"/>
+                  <param name="database_name" value="test-plasmindfinder-db"/>
+              </section>
+              <section name="output_files">
+                  <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>
+              </section>
+              <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/>
+              <output name="hit_file" value="test_1/Hit_in_genome_seq_test1.fsa" ftype="fasta"/>
+              <output name="plasmid_file" value="test_1/Plasmid_seqs_test1.fsa" ftype="fasta"/>
+              <output name="result_file" value="test_1/results_tab_test1.tsv"/>
+              <output name="raw_file" value="test_1/results_test1.txt" lines_diff="2"/>
+              <output name="log_file" value="test_1/logfile_test1.log" lines_diff="7"/>
+        </test>
+        <!--test_2 with default value and for fastq file -->
+        <test expect_num_outputs="4">
+              <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"/>
+              </section>
+              <section name="output_files">
+                  <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>
+              </section>
+              <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/>
+              <output name="result_file" value="test_2/results_tab_test2.tsv"/>
+              <output name="raw_file" value="test_2/results_test2.txt" lines_diff="2"/>
+              <output name="log_file" value="test_2/logfile_test2.log" lines_diff="7"/>
+        </test>
+        <!--test_3 with default value and for fastq file -->
+        <test expect_num_outputs="3">
+              <section name="input">
+                  <param name="input_file" value="contigs.fasta"/>
+                  <param name="input_type" value="genome"/>
+                  <param name="database_name" value="test-plasmindfinder-db"/>
+              </section>
+              <section name="options">
+                  <param name="min_cov" value="0.2" />
+                  <param name="threshold" value="0.6"/>
+              </section>
+              <section name="output_files">
+                  <param name="output_selection" value="hit_fasta,plasmid_fasta,result_tsv"/>
+              </section>
+              <output name="hit_file" value="test_3/Hit_in_genome_seq_test3.fsa" ftype="fasta"/>
+              <output name="plasmid_file" value="test_3/Plasmid_seqs_test3.fsa" ftype="fasta"/>
+              <output name="result_file" value="test_3/results_tab_test3.tsv"/>
+        </test>
+    </tests>
+    <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.
+      **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)
+      **Output**
+      Some output files are availables
+      - A fasta file with all available hits 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 log file with analysis parameters
+
+    ]]></help>
+      <expand macro="citations"/>
+</tool>