# HG changeset patch
# User matnguyen
# Date 1551771400 18000
# Node ID baf1e89b42eb1a31ec847d99a1ec4b43299fc773
# Parent  c1b6f5fbbcadd7f4c8a7063a2c399448b645670e
Added config builder

diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/concatenator/concatenator
--- a/galaxy/tools/concatenator/concatenator	Fri Feb 01 16:56:03 2019 -0500
+++ b/galaxy/tools/concatenator/concatenator	Tue Mar 05 02:36:40 2019 -0500
@@ -6,9 +6,18 @@
 parser = ap.ArgumentParser(prog='concatenater', conflict_handler='resolve',
                            description="Concatenates all accessions and their associated paths")
 
-input = parser.add_argument_group('Input', '')
-input.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)")
-input.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls")
+subparser = parser.add_subparsers(dest='subcommand')
+
+variant_parser = subparser.add_parser(name='variant', help="Concatenate variant call files")
+variant_parser.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)")
+variant_parser.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls")
+
+cluster_parser = subparser.add_parser('cluster')
+cluster_parser.add_argument('--mlst', metavar="MLST", type=str, help="MLST clusters/distance matrix")
+cluster_parser.add_argument('--snp', metavar="SNP", type=str, help="SNP clusters/distance matrix")
+cluster_parser.add_argument('--cnv', metavar="CNV", type=str, help="CNV clusters/distance matrix")
+cluster_parser.add_argument('--spoligo', metavar="SPOLIGO", type=str, help="Spoligotyping clusters/distance matrix")
+# cluster_parser.add_argument('--kwip', metavar="KWIP", type=str, help="Kwip clusters/distance matrix")
 
 if len(sys.argv) == 1:
     parser.print_usage()
@@ -17,5 +26,13 @@
 args = parser.parse_args()
 output = open('paths.txt', 'w')
 
-for index,path in enumerate(args.input):
-    output.write("%s=%s\n" % (args.name[index], path))
+if args.subcommand == 'variant':
+    for index,path in enumerate(args.input):
+        output.write("%s=%s\n" % (args.name[index], path))
+elif args.subcommand == 'cluster':
+    variant_types = [(args.mlst, 'MLST'), (args.snp, 'SNP'), (args.cnv, 'CNV'), (args.spoligo, 'spoligotyping')]
+    for variant in variant_types:
+        if variant[0] == None:
+            continue
+        else:
+            output.write("%s=%s\n" % (variant[1], variant[0]))
diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/concatenator/concatenator.xml
--- a/galaxy/tools/concatenator/concatenator.xml	Fri Feb 01 16:56:03 2019 -0500
+++ b/galaxy/tools/concatenator/concatenator.xml	Tue Mar 05 02:36:40 2019 -0500
@@ -5,12 +5,70 @@
     </requirements>
 
     <command><![CDATA[
-        $__tool_directory__/concatenator -n #for $path in $paths# ${path.element_identifier} #end for#
-        -i #for $path in $paths# $path #end for#
+        $__tool_directory__/concatenator
+
+        #if $input_type.input_type_selector == "variant"
+            variant
+            -n #for $path in $input_type.paths# ${path.element_identifier} #end for#
+            -i #for $path in $input_type.paths# $path #end for#
+        #elif $input_type.input_type_selector == "clustering"
+            cluster
+            #if $input_type.mlst.mlst_checkbox
+                --mlst $input_type.mlst.mlst_path
+            #end if
+            #if $input_type.snp.snp_checkbox
+                --snp $input_type.snp.snp_path
+            #end if
+            #if $input_type.cnv.cnv_checkbox
+                --cnv $input_type.cnv.cnv_path
+            #end if
+            #if $input_type.spoligo.spoligo_checkbox
+                --spoligo $input_type.spoligo.spoligo_path
+            #end if
+         #end if
     ]]></command>
 
+
     <inputs>
-        <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/>
+        <conditional name="input_type">
+            <param name="input_type_selector" type="select" label="Concatenation of variant calls, or clustering files">
+                <option value="variant">Variant Call Files</option>
+                <option value="clustering">Clustering/Distance Matrix Files</option>
+            </param>
+            <when value="variant">
+                <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/>
+            </when>
+            <when value="clustering">
+                <conditional name="mlst">
+                    <param name="mlst_checkbox" type="boolean" label="Include MLST"/>
+                    <when value="true">
+                        <param name="mlst_path" type="data" label="MLST Clustering/Distance Matrix file"
+                               format="txt,tabular"/>
+                    </when>
+                </conditional>
+                <conditional name="snp">
+                    <param name="snp_checkbox" type="boolean" label="Include SNP"/>
+                    <when value="true">
+                        <param name="snp_path" type="data" label="SNP Clustering/Distance Matrix file"
+                               format="txt,tabular"/>
+                    </when>
+                </conditional>
+                <conditional name="cnv">
+                    <param name="cnv_checkbox" type="boolean" label="Include CNV"/>
+                    <when value="true">
+                        <param name="cnv_path" type="data" label="CNV Clustering/Distance Matrix file"
+                               format="txt,tabular"/>
+                    </when>
+                </conditional>
+                <conditional name="spoligo">
+                    <param name="spoligo_checkbox" type="boolean" label="Include Spoligotyping"/>
+                    <when value="true">
+                        <param name="spoligo_path" type="data" label="Spoligotyping Clustering/Distance Matrix file"
+                               format="txt,tabular"/>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
     </inputs>
 
     <outputs>
diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/config_builder/config_builder
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy/tools/config_builder/config_builder	Tue Mar 05 02:36:40 2019 -0500
@@ -0,0 +1,185 @@
+#!/usr/bin/env python
+
+import sys
+import yaml
+import argparse as ap
+
+parser = ap.ArgumentParser(prog='config_builder', conflict_handler='resolve',
+                           description="Builds the config file for PathOGiST")
+
+parser.add_argument('yaml', help="Blank config file")
+parser.add_argument('forward', help="File to list of forward reads")
+parser.add_argument('reverse', help="File to list of reverse reads")
+parser.add_argument('output', help="Output prefix for final consensus clustering and visualization")
+
+tools = parser.add_argument_group('Tools')
+tools.add_argument('--snippy', action='store_true', help="Run Snippy")
+tools.add_argument('--kwip', action='store_true', help="Run Kwip")
+tools.add_argument('--prince', action='store_true', help="Run Prince")
+tools.add_argument('--spotyping', action='store_true', help="Run Spotyping")
+tools.add_argument('--mentalist', action='store_true', help="Run Mentalist")
+
+mentalist = parser.add_argument_group('Mentalist')
+mentalist.add_argument('--local_file', action='store_true', help="Use local database")
+mentalist.add_argument('--build_db', action='store_true', help="Build a database")
+mentalist.add_argument('--download_pubmlst', action='store_true', help="Download pubMLST scheme")
+mentalist.add_argument('--download_cgmlst', action='store_true', help="Download cgMLST scheme")
+mentalist.add_argument('--download_enterobase', action='store_true', help="Download Enterobase scheme")
+
+mentalist.add_argument('--local_db', metavar="STRING", help="Location of database")
+mentalist.add_argument('--kmer', metavar="INT", help="Kmer size")
+mentalist.add_argument('--fasta_files', metavar="STRING", help="Location of FASTA files for MLST scheme")
+mentalist.add_argument('--profile', metavar="STRING", help="Profile file for known genotypes")
+mentalist.add_argument('--scheme', metavar="STRING", help="Species name or scheme ID")
+mentalist.add_argument('--entero_scheme', metavar="STRING", help="(S)almonella, (Y)ersinia, or (E)scherichia/Shigella")
+mentalist.add_argument('--entero_type', metavar="STRING", help="'cg' or 'wg' for cgMLST or wgMLST, respectively.")
+mentalist.add_argument('--mutation_threshold', metavar="INT", help="Maximum number of mutations when looking for novel "
+                                                                   "alleles")
+mentalist.add_argument('--kt', metavar="INT", help="Minimum number of times a kmer is seen to be considered present "
+                                                   "in the sample")
+
+kwip = parser.add_argument_group('Kwip')
+kwip.add_argument('--N', metavar="INT", help="Number of tables")
+kwip.add_argument('--x', metavar="INT", help="Maximum table size")
+kwip.add_argument('--ksize', metavar="INT", help="kmer size to use")
+kwip.add_argument('--unique_kmers', metavar="INT", help="Approximate number of unique kmers in the input set")
+
+snippy = parser.add_argument_group('Snippy')
+snippy.add_argument('--reference', metavar="STRING", help="Reference genome. Supports FASTA, GenBank, EMBL (not GFF)")
+snippy.add_argument('--mapqual', metavar="INT", help="Minimum read mapping quality to consider")
+snippy.add_argument('--basequal', metavar="INT", help="Minimum base quality to consider")
+snippy.add_argument('--mincov', metavar="INT", help="Minimum coverage of variant site")
+snippy.add_argument('--minfrac', metavar="FLOAT", help="Minimum proportion for variant evidence")
+
+clustering = parser.add_argument_group('Clustering')
+clustering.add_argument('--fine_snp', action='store_true', help="Use SNP as a fine datatype")
+clustering.add_argument('--fine_mlst', action='store_true', help="Use MLST as a fine datatype")
+clustering.add_argument('--fine_kwip', action='store_true', help="Use Kwip as a fine datatype")
+clustering.add_argument('--fine_spoligo', action='store_true', help="Use Spoligotyping as a fine datatype")
+clustering.add_argument('--fine_cnv', action='store_true', help="Use CNV as a fine datatype")
+clustering.add_argument('--snp_thresh', metavar="INT", help="Threshold value for SNP")
+clustering.add_argument('--mlst_thresh', metavar="INT", help="Threshold value for MLST")
+clustering.add_argument('--kwip_thresh', metavar="INT", help="Threshold value for Kwip")
+clustering.add_argument('--spoligo_thresh', metavar="INT", help="Threshold value for Spoligotyping")
+clustering.add_argument('--cnv_thresh', metavar="INT", help="Threshold value for CNV")
+clustering.add_argument('--less_constraints', action='store_true', help="Use less constraints when clustering")
+clustering.add_argument('--method', metavar="STRING", help="Use `C4` or `ILP` as clustering method")
+clustering.add_argument('--no_presolve', action='store_true', help="Do not perform presolving")
+clustering.add_argument('--visualize', action='store_true', help="Visualize clusters")
+
+if len(sys.argv) == 1:
+    parser.print_usage()
+    sys.exit(1)
+
+args = parser.parse_args()
+
+with open(args.yaml) as f:
+    list_doc = yaml.load(f)
+
+for line in list_doc:
+    if line == 'temp':
+        list_doc[line] = 'tmp_dir'
+
+    if line == 'threads':
+        pass
+
+    if line == 'run':
+        if args.snippy:
+            list_doc[line]['snippy'] = 1
+        if args.kwip:
+            list_doc[line]['kwip'] = 1
+        if args.prince:
+            list_doc[line]['prince'] = 1
+        if args.spotyping:
+            list_doc[line]['spotyping'] = 1
+        if args.mentalist:
+            list_doc[line]['mentalist'] = 1
+
+    if line == 'genotyping':
+        # Forward and reverse reads
+        list_doc[line]['input_reads']['forward_reads'] = args.forward
+        list_doc[line]['input_reads']['reverse_reads'] = args.reverse
+
+        if args.mentalist:
+            if args.local_file:
+                list_doc[line]['mentalist']['local_file']['database'] = args.local_db
+            elif args.build_db:
+                list_doc[line]['mentalist']['build_db']['options']['k'] = args.kmer
+                list_doc[line]['mentalist']['build_db']['options']['fasta_files'] = args.fasta_files
+                list_doc[line]['mentalist']['build_db']['options']['profile'] = args.profile
+            elif args.download_pubmlst:
+                list_doc[line]['mentalist']['download_pubmlst']['options']['k'] = args.kmer
+                list_doc[line]['mentalist']['download_pubmlst']['options']['scheme'] = args.scheme
+            elif args.download_cgmlst:
+                list_doc[line]['mentalist']['download_cgmlst']['options']['k'] = args.kmer
+                list_doc[line]['mentalist']['download_cgmlst']['options']['scheme'] = args.scheme
+            elif args.download_enterobase:
+                list_doc[line]['mentalist']['download_enterobase']['options']['k'] = args.kmer
+                list_doc[line]['mentalist']['download_enterobase']['options']['scheme'] = args.entero_scheme
+                list_doc[line]['mentalist']['download_enterobase']['options']['type'] = args.entero_type
+
+            if args.mutation_threshold:
+                list_doc[line]['mentalist']['call']['options']['mutation_threshold'] = args.mutation_threshold
+            if args.kt:
+                list_doc[line]['mentalist']['call']['options']['kt'] = args.kt
+
+        if args.kwip:
+            if args.N:
+                list_doc[line]['kwip']['khmer_options']['N'] = args.N
+            if args.x:
+                list_doc[line]['kwip']['khmer_options']['x'] = args.x
+            if args.ksize:
+                list_doc[line]['kwip']['khmer_options']['ksize'] = args.ksize
+            if args.unique_kmers:
+                list_doc[line]['kwip']['khmer_options']['unique-kmers'] = args.unique_kmers
+
+        if args.snippy:
+            list_doc[line]['snippy']['options']['reference'] = args.reference
+            if args.mapqual:
+                list_doc[line]['snippy']['options']['mapqual'] = args.mapqual
+            if args.basequal:
+                list_doc[line]['snippy']['options']['basequal'] = args.basequal
+            if args.mincov:
+                list_doc[line]['snippy']['options']['mincov'] = args.mincov
+            if args.minfrac:
+                list_doc[line]['snippy']['options']['minfrac'] = args.minfrac
+
+    if line == 'clustering':
+        list_doc[line]['output_prefix'] = args.output
+
+        fine = []
+        if args.fine_snp:
+            fine.append('SNP')
+        if args.fine_mlst:
+            fine.append('MLST')
+        if args.fine_kwip:
+            fine.append('kWIP')
+        if args.fine_spoligo:
+            fine.append('spoligotyping')
+        if args.fine_cnv:
+            fine.append('CNV')
+        list_doc[line]['fine_clusterings'] = fine
+
+        if args.snp_thresh:
+            list_doc[line]['thresholds']['SNP'] = args.snp_thresh
+        if args.mlst_thresh:
+            list_doc[line]['thresholds']['MLST'] = args.snp_thresh
+        if args.kwip_thresh:
+            list_doc[line]['thresholds']['kWIP'] = args.snp_thresh
+        if args.spoligo_thresh:
+            list_doc[line]['thresholds']['spoligotyping'] = args.snp_thresh
+        if args.cnv_thresh:
+            list_doc[line]['thresholds']['CNV'] = args.snp_thresh
+
+        if args.less_constraints:
+            list_doc[line]['all_constraints'] = False
+        if args.method:
+            list_doc[line]['method'] = args.method
+        if args.no_presolve:
+            list_doc[line]['presolve'] = False
+        if args.visualize:
+            list_doc[line]['visualize'] = True
+
+with open("config.yaml", 'w') as f:
+    yaml.dump(list_doc, f)
+
diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/config_builder/config_builder.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy/tools/config_builder/config_builder.xml	Tue Mar 05 02:36:40 2019 -0500
@@ -0,0 +1,243 @@
+<tool id="config_builder" name="PathOGiST - Config Builder" version="1.0.0">
+    <description>: Creates and populates the config file to run PathOGiST</description>
+    <requirements>
+        <requirement type="package" version="0.2.3">pathogist</requirement>
+    </requirements>
+
+    <command><![CDATA[
+        PATHOGIST all config.yaml --new_config
+
+        $__tool_directory__/config_builder
+
+        #if snippy.snippy_checkbox
+            --snippy
+            --reference $snippy.reference
+            #if snippy.snippy_adv.snippy_adv_checkbox
+                --mapqual $snippy.mapqual
+                --basequal $snippy.basequal
+                --mincov $snippy.mincov
+                --minfrac $snippy.minfrac
+            #endif
+            $snippy.snp_fine
+            --snp_thresh $snippy.snp_threshold
+        #endif
+
+        #if mentalist.mentalist_checkbox
+            --mentalist
+            #if mentalist.db_loc.db_selector == "local_file"
+                --local_file
+                --local_db $mentalist.mlst_database
+            #endif
+            #if mentalist.db_loc.db_selector == "build_db"
+                --build_db
+                --kmer $mentalist.k
+                --fasta_files $mentalist.fasta_files
+                --profile $mentalist.profile
+            #endif
+            #if mentalist.db_loc.db_selector == "download_pubmlst"
+                --download_pubmlst
+                --kmer $mentalist.k
+                --scheme $mentalist.scheme
+            #endif
+            #if mentalist.db_loc.db_selector == "download_cgmlst"
+                --download_cgmlst
+                --kmer $mentalist.k
+                --scheme $mentalist.scheme
+            #endif
+            #if mentalist.db_loc.db_selector == "download_enterobase"
+                --download_enterobase $mentalist.k
+                --entero_scheme $mentalist.scheme
+                --entero_type $mentalist.type
+            #endif
+            #if mentalist.mentalist_adv.mentalist_adv_checkbox
+                --mutation_threshold $mentalist.mutation_thresh
+                --kt $mentalist.kt
+            #endif
+            $mentalist.mlst_fine
+            --mlst_thresh $mentalist.mlst_threshold
+        #endif
+
+        #if prince.prince_checkbox
+            --prince
+            $prince.cnv_fine
+            --cnv_thresh $prince.cnv_threshold
+        #endif
+
+        #if kwip.kwip_checkbox
+            --kwip
+            #if kwip.kwip_adv.kwip_adv_checkbox
+                --N $kwip.N
+                --x $kwip.x
+                --ksize $kwip.ksize
+                --unique_kmers $kwip.unique_kmers
+            #endif
+            $kwip.kwip_fine
+            --kwip_thresh $kwip.kwip_threshold
+        #endif
+
+        #if spotyping.spotyping_checkbox
+            --spotyping
+            $spotyping.spoligo_fine
+            --spoligo_thresh $spotyping.spoligo_threshold
+        #endif
+
+        #if adv_clustering.adv_clustering_checkbox
+            $adv_clustering.all_constraints
+            --method $adv_clustering.method
+            $adv_clustering.presolve
+            $adv_clustering.visualize
+        #endif
+    ]]></command>
+
+
+    <inputs>
+        <!--<conditional name="task">-->
+            <!--<param name="task_selector" type="select" label="Create Blank Config or Populate Config File">-->
+                <!--<option value="create">Create Blank Config File</option>-->
+                <!--<option value="populate">Populate Config File</option>-->
+            <!--</param>-->
+            <!--<when value="create">-->
+
+            <!--</when>-->
+            <!--<when value="populate">-->
+        <conditional name="snippy">
+            <param name="snippy_checkbox" type="boolean" label="Run Snippy"/>
+            <when value="true">
+                <param name="reference" type="data" format="fasta,fa,fasta.gz,fa.gz" label="Reference Genome"/>
+                <conditional name="snippy_adv">
+                    <param name="snippy_adv_checkbox" type="boolean" label="Advanced Snippy Parameters"/>
+                    <when value="true">
+                        <param name="mapqual" type="integer" value="60" min="0" label="Minimum read mapping
+                        quality to consider"/>
+                        <param name="basequal" type="integer" value="20" min="0" label="Minimum base quality
+                        to consider"/>
+                        <param name="mincov" type="integer" value="10" min="0" label="Minimum coverage of
+                        variant site"/>
+                        <param name="minfrac" type="float" value="0.9" min="0" label="Minimum proportion of
+                        variant evidence"/>
+                    </when>
+                </conditional>
+                <param name="snp_fine" type="boolean" label="Consider SNP as a fine datatype"/>
+                <param name="snp_threshold" type="integer" value="2500" min="0"
+                       label="Correlation clustering threshold for MLST"/>
+            </when>
+        </conditional>
+
+        <conditional name="mentalist">
+            <param name="mentalist_checkbox" type="boolean" label="Run MentaLiST"/>
+            <when value="true">
+                <conditional name="db_loc">
+                    <param name="db_selector" type="select" label="Option for obtaining MLST database">
+                        <option value="local_file">Local File</option>
+                        <option value="build_db">Build DB</option>
+                        <option value="download_pubmlst">Download PubMLST Scheme</option>
+                        <option value="download_cgmlst">Download cgMLST Scheme</option>
+                        <option value="download_enterobase">Download Enterobase Scheme</option>
+                    </param>
+                    <when value="local_file">
+                        <param name="mlst_database" format="db" type="data" label="MLST database file"/>
+                    </when>
+                    <when value="build_db">
+                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
+                        <param name="fasta_files" type="data" format="txt,tabular" label="List of FASTA files"/>
+                        <param name="profile" type="data" format="txt" label="Profile file for known
+                        genotypes"/>
+                    </when>
+                    <when value="download_pubmlst">
+                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
+                        <param name="scheme" type="text" label="Species name or scheme ID"/>
+                    </when>
+                    <when value="download_cgmlst">
+                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
+                        <param name="scheme" type="text" label="Species name or scheme ID"/>
+                    </when>
+                    <when value="download_enterobase">
+                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
+                        <param name="scheme" type="text" label="(S)almonella, (Y)ersinia, or
+                        (E)scherichia/Shigella"/>
+                        <param name="type" type="text" label="'cg' or 'wg' for cgMLST or wgMLST, respectively"/>
+                    </when>
+                </conditional>
+
+                <conditional name="mentalist_adv">
+                    <param name="mentalist_adv_checkbox" type="boolean" label="Advanced MentaLiST Parameters"/>
+                    <when value="true">
+                        <param name="mutation_thresh" type="integer" min="1" value="6" label="Maximum number of
+                        mutations when looking for novel alleles"/>
+                        <param name="kt" type="integer" value="10" min="1" label="Minimum number of times a
+                        kmer is seen to be considered present in the sample"/>
+                    </when>
+                </conditional>
+                <param name="mlst_fine" type="boolean" label="Consider MLST as a fine datatype"/>
+                <param name="mlst_threshold" type="integer" value="300" min="0"
+                       label="Correlation clustering threshold for MLST"/>
+            </when>
+        </conditional>
+
+        <conditional name="prince">
+            <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>
+            <when value="true">
+                <param name="cnv_fine" type="boolean" label="Consider CNV as a fine datatype"/>
+                <param name="cnv_threshold" type="integer" value="100" min="0"
+                       label="Correlation clustering threshold for CNV"/>
+            </when>
+        </conditional>
+
+        <conditional name="kwip">
+            <param name="kwip_checkbox" type="boolean" label="Run kWIP"/>
+            <when value="true">
+                <conditional name="kwip_adv">
+                    <param name="kwip_adv_checkbox" type="boolean" label="Advance kWIP Parameters"/>
+                    <when value="true">
+                        <param name="N" type="integer" value="1" min="1" label="Number of tables"/>
+                        <param name="x" type="float" value="1e9" min="1" label="Maximum table size"/>
+                        <param name="ksize" type="integer" value="31" min="1" label="kmer size"/>
+                        <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number
+                        of unique kmers in the input set"/>
+                    </when>
+                </conditional>
+                <param name="kwip_fine" type="boolean" label="Consider kWIP as a fine datatype"/>
+                <param name="kwip_threshold" type="float" value="0.4" min="0"
+                       label="Correlation clustering threshold for kWIP"/>
+            </when>
+        </conditional>
+
+        <conditional name="spotyping">
+            <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>
+            <when value="true">
+                <param name="spoligo_fine" type="boolean" label="Consider spoligotype as a fine datatype"/>
+                <param name="spoligo_threshold" type="integer" value="8" min="0"
+                       label="Correlation clustering threshold for Spoligotyping"/>
+            </when>
+        </conditional>
+
+        <conditional name="adv_clustering">
+            <param name="adv_clustering_checkbox" type="boolean"
+                   label="Advanced settings for correlation and consensus clustering"/>
+            <when value="true">
+                <param name="all_constraints" type="boolean" checked="true" falsevalue="--less_constraints"
+                       truevalue="" label="Use all constraints when performing clustering"/>
+                <param name="method" type="text" value="C4" size="3"
+                       label="`C4` or `ILP` method for clustering algorithm"/>
+                <param name="presolve" type="boolean" checked="true" falsevalue="--no_presolve" truevalue=""
+                       label="Perform presolving for clustering"/>
+                <param name="visualize" type="boolean" checked="false" falsevalue="" truevalue="--visualize"
+                       label="Visualize clusters"/>
+            </when>
+        </conditional>
+            <!--</when>-->
+        <!--</conditional>-->
+    </inputs>
+
+    <outputs>
+        <data name="output" label="PathOGiST Config File" format="yaml" from_work_dir="config.yaml"/>
+    </outputs>
+
+    <help>
+
+    </help>
+
+    <citations>
+
+    </citations>
+</tool>
diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/visualization/visualization.xml
--- a/galaxy/tools/visualization/visualization.xml	Fri Feb 01 16:56:03 2019 -0500
+++ b/galaxy/tools/visualization/visualization.xml	Tue Mar 05 02:36:40 2019 -0500
@@ -5,7 +5,7 @@
     </requirements>
 
     <command><![CDATA[
-        PATHOGIST vis $distance $sample $pdf
+        PATHOGIST visualize $distance $sample $pdf
     ]]></command>
 
     <inputs>