--- a/mlst.xml	Mon Feb 12 05:18:20 2018 -0500
+++ b/mlst.xml	Mon Oct 15 07:41:48 2018 -0400
@@ -1,28 +1,60 @@
-<tool id="mlst" name="MLST" version="2.10">
-    <requirements>
-        <requirement type="package" version="2.10">mlst</requirement>
-    </requirements>
+<tool id="mlst" name="MLST" version="@VERSION@">
+    <description>Scans genomes against PubMLST schemes.</description>
+    <macros>
+        <import>macros.xml</import>
+
+        <xml name="legacy_param">
+            <param argument="--legacy" type="boolean" truevalue="--legacy" falsevalue="" checked="true" label="Include allele header" help="Include allele header row in output table (requires scheme to be set)" />
+        </xml>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
 
-    <version_command>mlst --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+
+        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
+        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
+        #set $named_input_files = ''
+        #for $input_file in $input_files
+            ## Add single quotes around each input file identifier
+            #set $_input_file = "'{}'".format($input_file.element_identifier)
+            ln -s '${input_file}' ${_input_file} &&
+            #set $named_input_files = $named_input_files + ' ' + $_input_file
+        #end for
 
-    <command detect_errors="exit_code"><![CDATA[
-        mlst "$input_file" --nopath
-        #if $settings.advanced == "advanced"
-            #if $settings.min_dna_id
-                --minid=$settings.min_dna_id
+        mlst --nopath
+        --threads "\${GALAXY_SLOTS:-1}"
+        #if str($settings.advanced) == "advanced"
+            #if str($settings.minid)
+                --minid=$settings.minid
+            #end if
+            #if str($settings.mincov)
+                --mincov=$settings.mincov
+            #end if
+            #if $settings.novel
+                --novel '${novel_alleles}'
             #end if
-            #if $settings.min_dna_cov
-                --mincov=$settings.min_dna_cov
-            #end if
-            #if $settings.scheme
-                --scheme=$settings.scheme
+            #if str($settings.scheme_condition.set_scheme) == "auto"
+                #if str($settings.scheme_condition.minscore)
+                    --minscore=$settings.scheme_condition.minscore
+                #end if
+                #if str($settings.scheme_condition.exclude)
+                    --exclude '${settings.scheme_condition.exclude}'
+                #end if
+            #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"
+                #if str($settings.scheme_condition.scheme)
+                    --scheme='${settings.scheme_condition.scheme}'
+                #end if
+                $settings.scheme_condition.legacy
             #end if
         #end if
+        ${named_input_files}
         > "$report"
     ]]></command>
 
     <inputs>
-        <param type="data" name="input_file" format="fasta,genbank" />
+        <param type="data" name="input_files" format="fasta,genbank" multiple="true" />
         <conditional name="settings">
             <param name="advanced" type="select" label="Specify advanced parameters">
                 <option value="simple" selected="true">No, use program defaults.</option>
@@ -31,46 +63,242 @@
             <when value="simple">
             </when>
             <when value="advanced">
-                <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
-                <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
-                <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
+                <param argument="--minid" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
+                <param argument="--mincov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
+                <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />
+                <conditional name="scheme_condition">
+                    <param name="set_scheme" type="select" label="Automatically set MLST scheme">
+                        <option value="auto" selected="true">Automatic MLST scheme detection</option>
+                        <option value="list">Select from a list of MLST schemes</option>
+                        <option value="manual">Manually set MLST scheme</option>
+                    </param>
+                    <when value="auto">
+                        <param argument="--minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
+                        <param argument="--exclude" type="text" area="false" label="Exclude these schemes" help="Ignore these schemes from auto detection (comma sep. list) (default 'ecoli_2,abaumannii')" optional="true" />
+                    </when>
+                    <when value="list">
+                        <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
+                            <option value="achromobacter">achromobacter</option>
+                            <option value="vvulnificus">vvulnificus</option>
+                            <option value="cglabrata">cglabrata</option>
+                            <option value="sthermophilus_2">sthermophilus_2</option>
+                            <option value="mmassiliense">mmassiliense</option>
+                            <option value="bhampsonii">bhampsonii</option>
+                            <option value="afumigatus">afumigatus</option>
+                            <option value="ecloacae">ecloacae</option>
+                            <option value="brucella">brucella</option>
+                            <option value="spseudintermedius">spseudintermedius</option>
+                            <option value="kpneumoniae">kpneumoniae</option>
+                            <option value="edwardsiella">edwardsiella</option>
+                            <option value="chlamydiales">chlamydiales</option>
+                            <option value="leptospira_2">leptospira_2</option>
+                            <option value="neisseria">neisseria</option>
+                            <option value="vcholerae">vcholerae</option>
+                            <option value="orhinotracheale">orhinotracheale</option>
+                            <option value="paeruginosa">paeruginosa</option>
+                            <option value="lsalivarius">lsalivarius</option>
+                            <option value="leptospira">leptospira</option>
+                            <option value="sepidermidis">sepidermidis</option>
+                            <option value="mhyorhinis">mhyorhinis</option>
+                            <option value="bcc">bcc</option>
+                            <option value="yruckeri">yruckeri</option>
+                            <option value="suberis">suberis</option>
+                            <option value="yersinia">yersinia</option>
+                            <option value="taylorella">taylorella</option>
+                            <option value="kaerogenes">kaerogenes</option>
+                            <option value="xfastidiosa">xfastidiosa</option>
+                            <option value="bordetella">bordetella</option>
+                            <option value="cbotulinum">cbotulinum</option>
+                            <option value="hpylori">hpylori</option>
+                            <option value="mpneumoniae">mpneumoniae</option>
+                            <option value="sdysgalactiae">sdysgalactiae</option>
+                            <option value="efaecium">efaecium</option>
+                            <option value="aphagocytophilum">aphagocytophilum</option>
+                            <option value="ecoli_2">ecoli_2</option>
+                            <option value="ganatis">ganatis</option>
+                            <option value="mhyopneumoniae">mhyopneumoniae</option>
+                            <option value="bsubtilis">bsubtilis</option>
+                            <option value="tenacibaculum">tenacibaculum</option>
+                            <option value="campylobacter">campylobacter</option>
+                            <option value="ranatipestifer">ranatipestifer</option>
+                            <option value="mcaseolyticus">mcaseolyticus</option>
+                            <option value="csputorum">csputorum</option>
+                            <option value="csinensis">csinensis</option>
+                            <option value="dnodosus">dnodosus</option>
+                            <option value="koxytoca">koxytoca</option>
+                            <option value="soralis">soralis</option>
+                            <option value="bcereus">bcereus</option>
+                            <option value="wolbachia">wolbachia</option>
+                            <option value="saureus">saureus</option>
+                            <option value="hcinaedi">hcinaedi</option>
+                            <option value="clari">clari</option>
+                            <option value="leptospira_3">leptospira_3</option>
+                            <option value="sinorhizobium">sinorhizobium</option>
+                            <option value="pmultocida_multihost">pmultocida_multihost</option>
+                            <option value="ecoli">ecoli</option>
+                            <option value="pdamselae">pdamselae</option>
+                            <option value="pmultocida_rirdc">pmultocida_rirdc</option>
+                            <option value="bhyodysenteriae">bhyodysenteriae</option>
+                            <option value="cupsaliensis">cupsaliensis</option>
+                            <option value="efaecalis">efaecalis</option>
+                            <option value="shaemolyticus">shaemolyticus</option>
+                            <option value="rhodococcus">rhodococcus</option>
+                            <option value="pacnes">pacnes</option>
+                            <option value="szooepidemicus">szooepidemicus</option>
+                            <option value="pgingivalis">pgingivalis</option>
+                            <option value="cfetus">cfetus</option>
+                            <option value="bpilosicoli">bpilosicoli</option>
+                            <option value="kseptempunctata">kseptempunctata</option>
+                            <option value="streptomyces">streptomyces</option>
+                            <option value="smaltophilia">smaltophilia</option>
+                            <option value="ppentosaceus">ppentosaceus</option>
+                            <option value="cronobacter">cronobacter</option>
+                            <option value="mhaemolytica">mhaemolytica</option>
+                            <option value="cdiphtheriae">cdiphtheriae</option>
+                            <option value="vcholerae2">vcholerae2</option>
+                            <option value="chyointestinalis">chyointestinalis</option>
+                            <option value="borrelia">borrelia</option>
+                            <option value="abaumannii">abaumannii</option>
+                            <option value="arcobacter">arcobacter</option>
+                            <option value="csepticum">csepticum</option>
+                            <option value="mcanis">mcanis</option>
+                            <option value="pfluorescens">pfluorescens</option>
+                            <option value="lmonocytogenes">lmonocytogenes</option>
+                            <option value="sgallolyticus">sgallolyticus</option>
+                            <option value="cfreundii">cfreundii</option>
+                            <option value="mplutonius">mplutonius</option>
+                            <option value="vibrio">vibrio</option>
+                            <option value="bbacilliformis">bbacilliformis</option>
+                            <option value="ypseudotuberculosis">ypseudotuberculosis</option>
+                            <option value="vparahaemolyticus">vparahaemolyticus</option>
+                            <option value="mcatarrhalis">mcatarrhalis</option>
+                            <option value="bintermedia">bintermedia</option>
+                            <option value="sagalactiae">sagalactiae</option>
+                            <option value="kkingae">kkingae</option>
+                            <option value="bpseudomallei">bpseudomallei</option>
+                            <option value="bhenselae">bhenselae</option>
+                            <option value="spneumoniae">spneumoniae</option>
+                            <option value="vtapetis">vtapetis</option>
+                            <option value="senterica">senterica</option>
+                            <option value="mabscessus">mabscessus</option>
+                            <option value="sthermophilus">sthermophilus</option>
+                            <option value="brachyspira">brachyspira</option>
+                            <option value="mbovis">mbovis</option>
+                            <option value="hsuis">hsuis</option>
+                            <option value="spyogenes">spyogenes</option>
+                            <option value="cconcisus">cconcisus</option>
+                            <option value="cmaltaromaticum">cmaltaromaticum</option>
+                            <option value="abaumannii_2">abaumannii_2</option>
+                            <option value="aeromonas">aeromonas</option>
+                            <option value="miowae">miowae</option>
+                            <option value="shominis">shominis</option>
+                            <option value="otsutsugamushi">otsutsugamushi</option>
+                            <option value="hinfluenzae">hinfluenzae</option>
+                            <option value="clanienae">clanienae</option>
+                            <option value="sbsec">sbsec</option>
+                            <option value="scanis">scanis</option>
+                            <option value="msynoviae">msynoviae</option>
+                            <option value="hparasuis">hparasuis</option>
+                            <option value="magalactiae">magalactiae</option>
+                            <option value="chelveticus">chelveticus</option>
+                            <option value="fpsychrophilum">fpsychrophilum</option>
+                            <option value="ssuis">ssuis</option>
+                            <option value="cdifficile">cdifficile</option>
+                            <option value="cinsulaenigrae">cinsulaenigrae</option>
+                            <option value="blicheniformis">blicheniformis</option>
+                            <option value="slugdunensis">slugdunensis</option>
+                            <option value="plarvae">plarvae</option>
+                        </param>
+                        <expand macro="legacy_param" />
+                    </when>
+                    <when value="manual">
+                        <param name="scheme" type="text" area="false" label="MLST Scheme (manual)" help="Enter a MLST scheme to use (see output of 'MLST List' tool for a list of available schemes)" />
+                        <expand macro="legacy_param" />
+                    </when>
+                </conditional>
             </when>
         </conditional>
     </inputs>
 
     <outputs>
-        <data name="report" format="tabular" />
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: report.tsv"/>
+        <data name="novel_alleles" format="fasta" label="${tool.name} on ${on_string}: novel_alleles.fasta">
+            <filter>settings['advanced'] == "advanced" and settings['novel']</filter>
+        </data>
     </outputs>
 
     <tests>
         <!-- Basic test - will produce no results. -->
         <test>
-            <param name="input_file" value="Acetobacter.fna"/>
+            <param name="input_files" value="Acetobacter.fna"/>
             <param name="advanced" value="simple"/>
-            <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
+            <output name="report" ftype="tabular" file="output_noresults.txt"/>
         </test>
 
         <!-- Basic test - will produce results. -->
         <test>
-            <param name="input_file" value="MRSA0252_trimmed.fna"/>
+            <param name="input_files" value="MRSA0252_trimmed.fna"/>
             <param name="advanced" value="simple"/>
-            <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
+            <output name="report" ftype="tabular" file="output_mrsa.txt"/>
         </test>
 
         <!-- Advanced test - Min DNA Coverage 100 -->
         <test>
-            <param name="input_file" value="MRSA0252_trimmed.fna"/>
+            <param name="input_files" value="MRSA0252_trimmed.fna"/>
             <param name="advanced" value="advanced"/>
-            <param name="min_dna_cov" value="100"/>
-            <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
+            <param name="mincov" value="100"/>
+            <output name="report" ftype="tabular" file="output_mincov100.txt"/>
         </test>
 
         <!-- Advanced test - Min DNA ID 100 -->
         <test>
-            <param name="input_file" value="MRSA0252_trimmed.fna"/>
+            <param name="input_files" value="MRSA0252_trimmed.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="minid" value="100"/>
+            <output name="report" ftype="tabular" file="output_minid100.txt"/>
+        </test>
+
+        <!-- Advanced test - Manually set MLST scheme -->
+        <test>
+            <param name="input_files" value="MRSA0252_trimmed.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="set_scheme" value="manual"/>
+            <param name="scheme" value="saureus"/>
+            <param name="legacy" value="true"/>
+            <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
+        </test>
+
+        <!-- Advanced test - Set a MLST scheme from a list -->
+        <test>
+            <param name="input_files" value="MRSA0252_trimmed.fna"/>
             <param name="advanced" value="advanced"/>
-            <param name="min_dna_id" value="100"/>
-            <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
+            <param name="set_scheme" value="list"/>
+            <param name="scheme" value="saureus"/>
+            <param name="legacy" value="true"/>
+            <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
+        </test>
+
+        <!-- Advanced test - exclude scheme -->
+        <test>
+            <param name="input_files" value="MRSA0252_trimmed.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="set_scheme" value="auto"/>
+            <param name="exclude" value="saureus"/>
+            <param name="legacy" value="false"/>
+            <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/>
+        </test>
+
+        <!-- Advanced test - output novel alleles. -->
+        <test>
+            <param name="input_files" value="MRSA0252_trimmed_novel.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="minid" value="98"/>
+            <param name="novel" value="true"/>
+            <param name="set_scheme" value="manual"/>
+            <param name="scheme" value="saureus"/>
+            <param name="legacy" value="false"/>
+            <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/>
+            <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/>
         </test>
     </tests>
 
@@ -95,7 +323,7 @@
 
 **Without auto-detection**
 
-If you provide the 'scheme' parameter, it will print a fixed tabular output with a heading containing allele names specific to that scheme. To view a list of schemes, use the MLST List tool.
+If you choose to manually set the MLST scheme, it will print a fixed tabular output with a heading containing allele names specific to that scheme (adjustable with **Include allele header**). To view a list of schemes, use the MLST List tool.
 
 ::
 
@@ -103,30 +331,27 @@
 	NM003.fa  neisseria  11    2     3    4     3       8     4    6
 
 **Missing data**
+
 MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below:
 
-+--------+---------------------------+
-| Symbol | Meaning                   |
-+========+===========================+
-| n      | Exact intact allele       |
-+--------+---------------------------+
-| ~n     | Novel allele similar to n |
-+--------+---------------------------+
-| n,m    | Multiple alleles          |
-+--------+---------------------------+
-|  *-*   | Allele missing            |
-+--------+---------------------------+
++--------+---------------------------------------+
+| Symbol | Meaning                               |
++========+=======================================+
+| n      | Exact intact allele                   |
++--------+---------------------------------------+
+| ~n     | Novel full length allele similar to n |
++--------+---------------------------------------+
+| n?     | Partial match to known allele         |
++--------+---------------------------------------+
+| n,m    | Multiple alleles                      |
++--------+---------------------------------------+
+|  *-*   | Allele missing                        |
++--------+---------------------------------------+
+
+Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles.
 
 Galaxy wrapper maintained by Simon Gladman.
     ]]></help>
 
-    <citations>
-        <citation type="bibtex">
-            @UNPUBLISHED{Seemann2016,
-            author = "Seemann T",
-            title = "MLST: Scan contig files against PubMLST typing schemes",
-            year = "2016",
-            note = "https://github.com/tseemann/mlst"}
-        </citation>
-    </citations>
+    <expand macro="citations" />
 </tool>