# HG changeset patch
# User jjjjia
# Date 1535577950 14400
# Node ID 3dc84625d22c735ece1ed331c8d913f54da2a6fa
# Parent  573136f142b687b6a6922d8714e1074f69b02f58
planemo upload

diff -r 573136f142b6 -r 3dc84625d22c cpo_galaxy_tree.py
--- a/cpo_galaxy_tree.py	Wed Aug 29 15:10:44 2018 -0400
+++ b/cpo_galaxy_tree.py	Wed Aug 29 17:25:50 2018 -0400
@@ -25,7 +25,7 @@
 import pandas #conda pandas
 import optparse
 import os
-os.environ['QT_QPA_PLATFORM']='offscreen'
+#os.environ['QT_QPA_PLATFORM']='offscreen'
 import datetime
 import sys
 import time
@@ -40,8 +40,8 @@
 #parses some parameters
 parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...")
 parser.add_option("-t", "--tree", dest="treePath", type="string", default="./pipelineTest/tree.txt", help="absolute file path to phylip tree")    
-parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/distance.tab", help="absolute file path to distance matrix")
-parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tsv",help="absolute file path to metadata file")
+parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/dist.tabular", help="absolute file path to distance matrix")
+parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tabular",help="absolute file path to metadata file")
 parser.add_option("-o", "--output_file", dest="outputFile", type="string", default="tree.png", help="Output graphics file. Use ending 'png', 'pdf' or 'svg' to specify file format.")
 
 # sensitive data adder
@@ -185,7 +185,7 @@
         _results.TotalPlasmids = int(r.loc[r.index[i], 'Total Plasmids'])
         _results.plasmidBestMatch = str(r.loc[r.index[i], 'Plasmid Best Match'])
         _results.plasmididentity = str(r.loc[r.index[i], 'Plasmid Identity'])
-        _results.plasmidsharedhashes = float(r.loc[r.index[i], 'Plasmid Shared Hash'])
+        _results.plasmidsharedhashes = str(r.loc[r.index[i], 'Plasmid Shared Hash'])
         for j in range(0,_results.TotalPlasmids):
             _plasmid = plasmidObj()
             _plasmid.PlasmidsID =(((str(r.loc[r.index[i], 'Plasmids ID'])).split(";"))[j])