--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/serotypefinder.xml	Wed Jul 12 17:09:33 2023 +0000
@@ -0,0 +1,61 @@
+<tool id="serotypefinder" name="serotypefinder" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <requirements>
+        <requirement type="package">serotypefinder</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+
+    #if $reads.reads_select == 'collection'
+      #set $name = $reads.coll.name.replace(' ', '_')
+      #set $forward = $reads.coll.forward
+      #set $reverse = $reads.coll.reverse
+      #set $infile = $name + "_1.fastq " +  $name + "_2.fastq" 
+      #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
+        gunzip -c $reverse > reverse.fastq;
+        #set $reverse = './reverse.fastq'
+        gunzip -c $forward > forward.fastq;
+        #set $forward = './forward.fastq'
+      #end if
+      ln -s $forward ${name}_1.fastq;
+      ln -s $reverse ${name}_2.fastq;
+   #else 
+      #set $name = $reads.assembly.name.replace(' ', '_')
+      #set $ga = $reads.assembly
+      #set $infile = $name + ".fasta" 
+      ln -s $ga ${name}.fasta;
+    #end if
+    serotypefinder -x -i $infile
+
+    ]]></command>
+    <inputs>
+        <conditional name="reads">
+            <param name="reads_select" type="select" label="Genome assembly or paired-end collection">
+                <option value="collection">Paired collection from your history</option>
+                <option value="genome">Genome Assembly</option>
+            </param>
+            <when value="collection">
+                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
+            </when>
+            <when value="genome">
+                <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="results" format="tabular" from_work_dir="results_tab.tsv" />
+    </outputs>
+  <help><![CDATA[
+    Serotype predictions for E.coli.
+  ]]></help>
+    <citations>
+       <citation type="bibtex">
+         @misc{fleming,
+         title={serotypefinder - Serotype Prediction for E. coli},
+         journal={epub}, publisher={epub},
+         author={Scheutz, Flemming},
+         year={2023}, month={Max},
+         url={https://bitbucket.org/genomicepidemiology/serotypefinder/src/master}},
+
+       </citation>
+    </citations>
+</tool>
+