# HG changeset patch
# User matnguyen
# Date 1552088551 18000
# Node ID a39471bf7d132944493fe9f56089b8f73dbc8216
# Parent  343bce47219b68eae65f571eb5948e650d1d7e27
Update to pathogist0.3

diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/concatenator/concatenator.xml
--- a/galaxy/tools/concatenator/concatenator.xml	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/concatenator/concatenator.xml	Fri Mar 08 18:42:31 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="concatenator" name="Concatenator" version="1.0.0">
     <description>creates a list of accessions and the associated path to their variant calls</description>
     <requirements>
-        <requirement type="package" version="0.2.3">pathogist</requirement>
+        <requirement type="package" version="0.3">pathogist</requirement>
     </requirements>
 
     <command><![CDATA[
diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/config_builder/config_builder
--- a/galaxy/tools/config_builder/config_builder	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/config_builder/config_builder	Fri Mar 08 18:42:31 2019 -0500
@@ -3,11 +3,11 @@
 import sys
 import yaml
 import argparse as ap
+import subprocess
 
 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")
@@ -73,7 +73,9 @@
 
 args = parser.parse_args()
 
-with open(args.yaml) as f:
+print(subprocess.check_output(['PATHOGIST', 'all', 'blank_config.yaml', '--new_config']))
+
+with open('blank_config.yaml') as f:
     list_doc = yaml.load(f)
 
 for line in list_doc:
diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/config_builder/config_builder.xml
--- a/galaxy/tools/config_builder/config_builder.xml	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/config_builder/config_builder.xml	Fri Mar 08 18:42:31 2019 -0500
@@ -1,12 +1,10 @@
 <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>
+        <requirement type="package" version="0.3">pathogist</requirement>
     </requirements>
 
     <command><![CDATA[
-        PATHOGIST all blank_config.yaml --new_config
-
         $__tool_directory__/config_builder
 
         #if $snippy.snippy_checkbox
@@ -88,7 +86,6 @@
             $adv_clustering.visualize
         #end if
 
-        blank_config.yaml
         $forward
         $reverse
         config.yaml
diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/consensus_clustering/consensus_clustering.xml
--- a/galaxy/tools/consensus_clustering/consensus_clustering.xml	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/consensus_clustering/consensus_clustering.xml	Fri Mar 08 18:42:31 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="consensus_clustering" name="PathOGiST - Consensus Clustering" version="1.0.0">
     <description>: Performs consensus clustering on multiple clusterings</description>
     <requirements>
-        <requirement type="package" version="0.2.3">pathogist</requirement>
+        <requirement type="package" version="0.3">pathogist</requirement>
     </requirements>
 
     <command><![CDATA[
diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/correlation_clustering/correlation_clustering.xml
--- a/galaxy/tools/correlation_clustering/correlation_clustering.xml	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/correlation_clustering/correlation_clustering.xml	Fri Mar 08 18:42:31 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0">
     <description>: Runs correlation clustering on a distance matrix file</description>
     <requirements>
-        <requirement type="package" version="0.2.3">pathogist</requirement>
+        <requirement type="package" version="0.3">pathogist</requirement>
     </requirements>
 
     <command><![CDATA[
diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/distance/distance.xml
--- a/galaxy/tools/distance/distance.xml	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/distance/distance.xml	Fri Mar 08 18:42:31 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="distance" name="PathOGiST - Distance" version="1.0.0">
     <description>: Construct distance matrix from genotyping data</description>
     <requirements>
-        <requirement type="package" version="0.2.3">pathogist</requirement>
+        <requirement type="package" version="0.3">pathogist</requirement>
     </requirements>
 
     <command><![CDATA[
diff -r 343bce47219b -r a39471bf7d13 galaxy/tools/visualization/visualization.xml
--- a/galaxy/tools/visualization/visualization.xml	Tue Mar 05 03:59:00 2019 -0500
+++ b/galaxy/tools/visualization/visualization.xml	Fri Mar 08 18:42:31 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="visualization" name="PathOGiST - Visualization" version="1.0.0">
     <description>: Visualize distance matrix</description>
     <requirements>
-        <requirement type="package" version="0.2.3">pathogist</requirement>
+        <requirement type="package" version="0.3">pathogist</requirement>
     </requirements>
 
     <command><![CDATA[