--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isescan.xml	Tue Aug 23 10:01:31 2022 +0000
@@ -0,0 +1,90 @@
+<tool id="isescan" name="ISEScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description> Insertion Sequence Elements detection in prokaryotic genomes </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        isescan.py
+        --seqfile '$input_file'
+        --output 'results'
+        $remove_short_is
+        --nthread \${GALAXY_SLOTS:-7}
+        | tee '$logfile'
+
+    ]]>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,fasta.gz" label="Genome fasta input" help="Fasta sequence to analyse for IS"/>
+        <param name="remove_short_is" argument="--removeShortIS" type="boolean" truevalue="--removeShortIS" falsevalue=""
+               label="Remove incomplete IS elements"
+               help="Remove partial IS elements which include IS element with length &gt; 400 or single copy IS element without perfect TIR"/>
+        <param name="output_format" type="select" label="Output format type" help="Choose an output file format">
+            <option value="raw"> Raw format (txt) </option>
+            <option value="csv"> Coma separate file (CSV) </option>
+            <option value="tsv" selected="true"> Tabular separate file (TSV) </option>
+        </param>
+        <param name="log_activate" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Keep the log file"/>
+    </inputs>
+    <outputs>
+        <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary of detected IS"/>
+        <data name="is_results" format="tabular" label="${tool.name} on ${on_string}: IS detected">
+          <change_format>
+              <when input="output_format" value="raw" format="txt"/>
+              <when input="output_format" value="csv" format="csv"/>
+              <when input="output_format" value="tsv" format="tabular"/>
+          </change_format>
+        </data>
+        <data name="gff_file" format="gff3" label="IS annotation"/>
+        <data name="is_fasta" format="fasta" label="${tool.name} on ${on_string}: IS nucleic sequence"/>
+        <data name="tpase_fasta" format="fasta" label="${tool.name} on ${on_string}: Transposase nucleic acid sequence"/>
+        <data name="tpase_amino" format="fasta" label="${tool.name} on ${on_string}: Transposase amino acid sequence"/>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log file">
+            <filter> log_activate == True </filter>
+        </data>
+    </outputs>
+    <tests>
+        <test> <!-- TEST_1 default parameters -->
+            <param name="input_file" value="NC_012624.fna" />
+            <output name="summary" value="TEST_1/test_1.fna.sum"/>
+            <output name="is_results" value="TEST_1/test_1.fna.tsv"/>
+            <output name="gff_file" value="TEST_1/test_1.fna.gff"/>
+            <output name="is_fasta" value="TEST_1/test_1.fna.is.fna"/>
+            <output name="tpase_fasta" value="TEST_1/test_1.fna.orf.fna"/>
+            <output name="tpase_amino" value="TEST_1/test_1.fna.orf.faa"/>
+            <output name="logfile" value="TEST_1/test_1.log" lines_diff="50"/>
+        </test>
+        <test> <!-- TEST_2 with remove_short_is and raw output-->
+            <param name="input_file" value="NC_012624.fna"/>
+            <param name="remove_short_is" value="true"/>
+            <param name="output_format" value="raw"/>
+            <output name="summary" value="TEST_2/test_2.fna.sum"/>
+            <output name="is_results" value="TEST_2/test_2.fna.raw"/>
+            <output name="gff_file" value="TEST_2/test_2.fna.gff"/>
+            <output name="is_fasta" value="TEST_2/test_2.fna.is.fna"/>
+            <output name="tpase_fasta" value="TEST_2/test_2.fna.orf.fna"/>
+            <output name="tpase_amino" value="TEST_2/test_2.fna.orf.faa"/>
+            <output name="logfile" value="TEST_2/test_2.log" lines_diff="50"/>
+        </test>
+        <test> <!-- TEST_3 without logfile and with csv output-->
+            <param name="input_file" value="NC_012624.fna"/>
+            <param name="remove_short_is" value="false"/>
+            <param name="output_format" value="csv"/>
+            <param name="log_activate" value="False"/>
+            <output name="summary" value="TEST_3/test_3.fna.sum"/>
+            <output name="is_results" value="TEST_3/test_3.fna.tsv"/>
+            <output name="gff_file" value="TEST_3/test_3.fna.gff"/>
+            <output name="is_fasta" value="TEST_3/test_3.fna.is.fna"/>
+            <output name="tpase_fasta" value="TEST_3/test_3.fna.orf.fna"/>
+            <output name="tpase_amino" value="TEST_3/test_3.fna.orf.faa"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **What it does**
+        With
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>