--- a/eurl_vtec_wgs_pt.xml	Wed Jan 22 09:10:12 2020 -0500
+++ b/eurl_vtec_wgs_pt.xml	Tue Jan 28 10:42:31 2020 -0500
@@ -1,18 +1,18 @@
-<tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="2.3">
-    <description>performs various typing tools test cfsan
-    </description>
+<tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="3.0">
+    <description>performs various typing tools</description>
     <requirements>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package">scipy</requirement>
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="5.26">perl</requirement>
         <requirement type="package">perl-bioperl</requirement>
         <requirement type="package" version="2.3.5">bowtie2</requirement>
         <requirement type="package" version="1.3.1">samtools</requirement>
         <requirement type="package" version="1.3.1">bcftools</requirement>
         <requirement type="package">bwa</requirement>
-        <requirement type="package">blast</requirement>
+        <requirement type="package">mmseqs2</requirement>
         <requirement type="package">spades</requirement>
         <requirement type="package">fastqc</requirement>
-        <requirement type="package">mentalist</requirement>
+        <requirement type="package" version="0.2.4">mentalist</requirement>
+		<requirement type="package" version="3.6.7">ncbi-amrfinderplus</requirement>
     </requirements>
     <!-- basic error handling -->
     <stdio>
@@ -24,25 +24,25 @@
       #if str( $library.type ) == "single":
 	      -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${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} 
-          --text1 $text_file_1 --trimmed1 $trimmed1
+          --text1 $text_file_1
       #elif str( $library.type ) == "paired":
 	      -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${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} 
-          --text1 $text_file_1 --trimmed1 $trimmed1
+          --text1 $text_file_1
           -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${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} 
-          --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
+          --text2 $text_file_2
       #elif str( $library.type ) == "pairedcollection":
 	      -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}' 
           --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} 
-          --text1 $text_file_1 --trimmed1 $trimmed1
+          --text1 $text_file_1
           -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}' 
           --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} 
-          --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
+          --text2 $text_file_2
       #end if
       #if $serotyping:
           --serotyping
-          --spades_log $spades_log --blastn_O $blastn_O --blastn_H $blastn_H
+          --antigen_O $antigen_O --antigen_H $antigen_H
       #end if         
       #if $virulotyping:
           --virulotyping
@@ -50,7 +50,12 @@
       #end if
       #if $shigatoxintyping:
           --shigatoxintyping
-          --blastn_STX $blastn_STX
+          --stx $stx
+      #end if
+      #if $amrtyping:
+          --amrtyping
+          --amr $amr
+		  --amr_id $__app__.security.encode_id($amr.dataset.id)
       #end if
     </command>
 
@@ -76,6 +81,7 @@
         <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
         <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
         <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
+        <param name="amrtyping" type="boolean" checked="true" label="Perform AMR typing" help="" />
     </inputs>
 
     <!-- define outputs -->
@@ -88,34 +94,22 @@
         <data format="txt" name="text_file_2"  label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
             <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
         </data>
-        <data name="trimmed1" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed 
-                #if str( $library.type ) == 'paired'#
-                    forward
-                #end if#
-            FASTQ">
-        </data>
-        <data name="trimmed2" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed reverse FASTQ">
-            <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
-        </data>
-        <data name="trimmedunpaired" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed unpaired reads">
-            <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
-        </data>
         <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
-        <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}: Mapping reads" hidden="true">
+        <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}" hidden="true">
             <filter>virulotyping</filter>
         </data>
-        <data name="blastn_STX" format="tabular" label="Blastn for Shiga toxin on ${on_string}" hidden="true" >
+        <data name="stx" format="tabular" label="Shiga toxin subtyper on ${on_string}" hidden="true" >
             <filter>shigatoxintyping</filter>
         </data>
-        <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}: Alleles Table" hidden="true" />
-        <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
+        <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}" hidden="true" />
+        <data name="antigen_O" format="tabular" label="Antigen_O typer on ${on_string}" hidden="true">
             <filter>serotyping</filter>
         </data>
-        <data name="blastn_O" format="tabular" label="Blastn for O on ${on_string}" hidden="true">
+        <data name="antigen_H" format="tabular" label="Antigen_H typer on ${on_string}" hidden="true">
             <filter>serotyping</filter>
         </data>
-        <data name="blastn_H" format="tabular" label="Blastn for H on ${on_string}" hidden="true">
-            <filter>serotyping</filter>
+        <data name="amr" format="tabular" label="AMR typer on ${on_string}" hidden="true">
+            <filter>amrtyping</filter>
         </data>
         <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
     </outputs>
@@ -134,8 +128,8 @@
                     <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" />
+            <output name="antigen_O" file="antigen_O" ftype="tabular" />
+            <output name="antigen_H" file="antigen_H" ftype="tabular" />
         </test>
     </tests>
 
@@ -147,17 +141,17 @@
 
 - Trimming (FASTQ positional and quality trimming)
 
+- Assembly (SPAdes)
+
 - Virulotyping (patho_typing tool from the INNUENDO Project)
 
 - Multi Locus Sequence Typing (MentaLiST 7 loci)
 
-- Filtering (DUK)
-
-- Assembly (SPAdes)
+- Serotyping (mmseqs2)
 
-- Serotyping (blastn)
+- Shigatoxintyping (mmseqs2 against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU)
 
-- Shigatoxintyping (blastn against the shiga toxin subtype database from the Statens Serum Institut (SSI) and Technical University of Denmark DTU)
+- AMR typing (AMRFinderPlus)
 
 Istituto Superiore di Sanità
 
@@ -181,21 +175,9 @@
       <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
       <citation type="doi">10.1038/nmeth.1923</citation>
       <citation type="doi">10.1099/mgen.0.000146</citation>
-      <citation type="bibtex">@ARTICLE{li-copeland,
-            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{edwards_ra,
-            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">10.1038/s41467-018-04964-5</citation>
+	  <citation type="doi">10.1128/AAC.00483-19</citation>
       <citation type="doi">10.1128/JCM.00008-15</citation>
     </citations>
 </tool>