# HG changeset patch
# User matnguyen
# Date 1552194429 18000
# Node ID 4bfb3a8dd9559108ce5ab8a9b292616d8c164109
# Parent  a39471bf7d132944493fe9f56089b8f73dbc8216
Bug fixes

diff -r a39471bf7d13 -r 4bfb3a8dd955 galaxy/tools/config_builder/config_builder
--- a/galaxy/tools/config_builder/config_builder	Fri Mar 08 18:42:31 2019 -0500
+++ b/galaxy/tools/config_builder/config_builder	Sun Mar 10 00:07:09 2019 -0500
@@ -3,7 +3,11 @@
 import sys
 import yaml
 import argparse as ap
-import subprocess
+import urllib.request as urllib
+
+# Version of PathOGiST
+MAJOR_VERSION = 0
+MINOR_VERSION = 3
 
 parser = ap.ArgumentParser(prog='config_builder', conflict_handler='resolve',
                            description="Builds the config file for PathOGiST")
@@ -73,7 +77,8 @@
 
 args = parser.parse_args()
 
-print(subprocess.check_output(['PATHOGIST', 'all', 'blank_config.yaml', '--new_config']))
+urllib.urlretrieve("https://github.com/WGS-TB/PathOGiST/releases/download/v{0}.{1}/blank_config.yaml"
+                   .format(MAJOR_VERSION, MINOR_VERSION), 'blank_config.yaml')
 
 with open('blank_config.yaml') as f:
     list_doc = yaml.load(f)
diff -r a39471bf7d13 -r 4bfb3a8dd955 galaxy/tools/config_builder/config_builder.xml
--- a/galaxy/tools/config_builder/config_builder.xml	Fri Mar 08 18:42:31 2019 -0500
+++ b/galaxy/tools/config_builder/config_builder.xml	Sun Mar 10 00:07:09 2019 -0500
@@ -113,7 +113,8 @@
                         variant evidence"/>
                     </when>
                 </conditional>
-                <param name="snp_fine" type="boolean" label="Consider SNP as a fine datatype"/>
+                <param name="snp_fine" type="boolean" checked="true" falsevalue="" truevalue="--fine_snp"
+                       label="Consider SNP as a fine datatype"/>
                 <param name="snp_threshold" type="integer" value="2500" min="0"
                        label="Correlation clustering threshold for MLST"/>
             </when>
@@ -164,7 +165,8 @@
                         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_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_mlst"
+                       label="Consider MLST as a fine datatype"/>
                 <param name="mlst_threshold" type="integer" value="300" min="0"
                        label="Correlation clustering threshold for MLST"/>
             </when>
@@ -173,7 +175,8 @@
         <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_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_cnv"
+                       label="Consider CNV as a fine datatype"/>
                 <param name="cnv_threshold" type="integer" value="100" min="0"
                        label="Correlation clustering threshold for CNV"/>
             </when>
@@ -192,7 +195,8 @@
                         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_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_kwip"
+                       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>
@@ -201,7 +205,8 @@
         <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_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_spoligo"
+                       label="Consider spoligotype as a fine datatype"/>
                 <param name="spoligo_threshold" type="integer" value="8" min="0"
                        label="Correlation clustering threshold for Spoligotyping"/>
             </when>