--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecoliserotyper.xml	Mon Jan 20 10:50:35 2020 -0500
@@ -0,0 +1,151 @@
+<tool id="ecoliserotyper" name="E coli Serotyper" version="1.2">
+    <description>performs serotyping of Escherichia coli
+    </description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.4">scipy</requirement>
+        <requirement type="package" version="5.26">perl</requirement>
+        <requirement type="package" version="1.7.2">perl-bioperl</requirement>
+        <requirement type="package" version="2.3.4">bowtie2</requirement>
+        <requirement type="package" version="1.3.1">samtools</requirement>
+        <requirement type="package" version="1.3.1">bcftools</requirement>
+        <requirement type="package" version="0.7.8">bwa</requirement>
+        <requirement type="package" version="2.7.1">blast</requirement>
+        <requirement type="package" version="3.12.0">spades</requirement>
+        <requirement type="package" version="0.11.8">fastqc</requirement>
+    </requirements>
+    <!-- basic error handling -->
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command>
+      python
+      $__tool_directory__/Ecoli_Serotyper.py --input_type ${origin.input_type} --log $logfile --output $report_out --blastn_O $blastn_O --blastn_H $blastn_H
+      #if str( $origin.input_type ) == "contigs":
+          -1 $origin.input_1 --input1_name '$origin.input_1.name' 
+      #else:
+          -1 $origin.library.input_1 --input1_ext ${origin.library.input_1.ext} --input1_name '${origin.library.input_1.name}' 
+          --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} 
+          --spades_log $spades_log
+          #if str( $origin.library.type ) == "paired":
+              -2 $origin.library.input_2 --input2_ext ${origin.library.input_2.ext} --input2_name '${origin.library.input_2.name}' 
+              --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} 
+          #end if
+      #end if
+    </command>
+
+    <inputs>
+        <!-- fastq/contigs -->
+        <conditional name="origin">
+                <param name="input_type" type="select" label="Are the input files FASTQ or Contigs">
+                  <option value="fastq">FASTQ</option>
+                  <option value="contigs">Contigs</option>
+                </param>
+
+                <when value="fastq">
+                    <!-- single/paired -->
+                    <conditional name="library">
+                        <param name="type" type="select" label="Is this single or paired library">
+                          <option value="single">Single-end</option>
+                          <option value="paired">Paired-end</option>
+                        </param>
+            
+                        <when value="single">
+                            <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
+                        </when>
+                        <when value="paired">
+                            <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
+                            <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
+                        </when>
+                    </conditional>
+                </when>
+                <when value="contigs">
+                    <param name="input_1" format="fasta" type="data" label="FASTA Contigs file" help="Must be of datatype &quot;fasta&quot;" />
+               </when>
+        </conditional>
+    </inputs>
+
+    <!-- define outputs -->
+    <outputs>
+        <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true">
+            <filter>origin['input_type'] == 'fastq'</filter>
+        </data>
+        <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
+            <filter>origin['input_type'] == 'fastq' and origin['library']['type'] == 'paired'</filter>
+        </data>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
+        <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
+            <filter>origin['input_type'] == 'fastq'</filter>
+        </data>
+        <data name="blastn_O" format="tabular" label="Blastn for O" hidden="true" />
+        <data name="blastn_H" format="tabular" label="Blastn for H" hidden="true" />
+        <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
+    </outputs>
+
+    <tests>
+        <test>
+            <!-- basic test on contigs file -->
+            <param name="input_type" value="contigs"/>
+            <param name="input_1" value="a_contigs.fasta" ftype="fasta"/>
+            <param name="input1_name" value="a_contigs.fasta"/>
+            <output name="report_out">
+                <assert_contents>
+                    <has_text text="wzx_208_AF529080_O26" />
+                    <has_text text="wzy_192_AF529080_O26" />
+                    <has_text text="fliC_269_AY337465_H11" />
+                    <has_text text="fliC_276_AY337472_H11" />
+                </assert_contents>
+            </output>
+            <output name="blastn_O" file="blastn_O" ftype="tabular" />
+            <output name="blastn_H" file="blastn_H" ftype="tabular" />
+        </test>
+    </tests>
+
+    <help>
+**E coli Serotyper Overview**
+
+This tool performs various operations:
+
+- Optionally: Quality assessment (FastQC)
+
+- Optionally: Trimming (FASTQ positional and quality trimming)
+
+- Optionally: Filtering (DUK)
+
+- Optionally: Assembly (SPAdes)
+
+- Serotyping (Blast+ against serotype databases from the Center for Genomic Epidemiology CGE)
+
+Istituto Superiore di Sanita'
+
+European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
+
+Developer: Arnold Knijn arnold.knijn@iss.it
+
+    </help>
+    <citations>
+      <citation type="bibtex">@ARTICLE{andrews_s,
+            author = {Andrews, S},
+            keywords = {bioinformatics, ngs, qc},
+            priority = {2},
+            title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
+            url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
+        }</citation>
+      <citation type="bibtex">@ARTICLE{andrews_s,
+            author = {Li, M, Copeland, A, and Han, J},
+            keywords = {bioinformatics, ngs},
+            title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
+            url = {https://www.osti.gov/servlets/purl/1016000/}
+        }</citation>
+      <citation type="bibtex">@ARTICLE{andrews_s,
+            author = {Edwards, RA},
+            keywords = {bioinformatics, ngs},
+            title = {{fastq-pair}},
+            url = {https://github.com/linsalrob/EdwardsLab/}
+        }</citation>
+      <citation type="doi">10.1089/cmb.2012.0021</citation>
+      <citation type="doi">10.1186/1471-2105-10-421</citation>
+      <citation type="doi">10.1186/s13742-015-0080-7</citation>
+      <citation type="doi">10.1128/JCM.00008-15</citation>
+    </citations>
+</tool>