--- a/cpo_galaxy_predictions.xml	Fri Aug 24 16:54:25 2018 -0400
+++ b/cpo_galaxy_predictions.xml	Fri Aug 24 19:10:42 2018 -0400
@@ -7,7 +7,7 @@
 	<command detect_errors="exit_code">
     <![CDATA[
 	    python '$__tool_directory__/cpo_galaxy_prediction.py'
-		'-i $ID'
+		'-i $contig.element_identifier'
 		'-m $mlst'
 		'-c $mobsuitecontig'
 		'-f $mobsuiteaggregate'
@@ -19,7 +19,7 @@
     ]]>
 	</command>
     <inputs>
-        <param type="text" name="ID"/>
+        <param type="data" name="contig"/>
         <param type="data" name="mlst" format="tabular" />
         <param type="data" name="mobsuitecontig" format="tabular" />
         <param type="data" name="mobsuiteaggregate" format="tabular" />

--- a/cpo_galaxy_tree.py	Fri Aug 24 16:54:25 2018 -0400
+++ b/cpo_galaxy_tree.py	Fri Aug 24 19:10:42 2018 -0400
@@ -18,6 +18,7 @@
 #		<requirement type="package" version="3.6">python</requirement>
 #       <requirement type="package" version="3.1.1">ete3</requirement>
 #		<requirement type="package" version="5.6.0">pyqt</requirement>
+#		<requirement type="package" version="5.6.2">qt</requirement>
 #  </requirements>
 
 import subprocess
@@ -53,17 +54,17 @@
 class workflowResult(object):
     def __init__(self):
         self.new = False
-        self.ID	= "" 
-        self.ExpectedSpecies = ""
-        self.MLSTSpecies = ""
-        self.SequenceType = ""
-        self.MLSTScheme = ""
-        self.CarbapenemResistanceGenes =""
-        self.OtherAMRGenes=""
-        self.TotalPlasmids = 0
+        self.ID	= "?" 
+        self.ExpectedSpecies = "?"
+        self.MLSTSpecies = "?"
+        self.SequenceType = "?"
+        self.MLSTScheme = "?"
+        self.CarbapenemResistanceGenes ="?"
+        self.OtherAMRGenes="?"
+        self.TotalPlasmids = -1
         self.plasmids = []
-        self.DefinitelyPlasmidContigs =""
-        self.LikelyPlasmidContigs=""
+        self.DefinitelyPlasmidContigs ="?"
+        self.LikelyPlasmidContigs="?"
         self.row = ""
 class plasmidObj(object):
     def __init__(self):
@@ -128,13 +129,15 @@
     _worflowResult = {}
     r = pandas.read_csv(pathToResult, delimiter='\t', header=0) 
     r = r.replace(numpy.nan, '', regex=True)
+    _naResult = workflowResult()
+    _worflowResult["na"] = _naResult
     for i in range(len(r.index)):  
         _results = workflowResult()
         if(str(r.loc[r.index[i], 'new']).lower() == "new"):
             _results.new = True
         else:
             _results.new = False        
-        _results.ID = str(r.loc[r.index[i], 'ID'])
+        _results.ID = str(r.loc[r.index[i], 'ID']).replace(".fa","")
         _results.ExpectedSpecies = str(r.loc[r.index[i], 'Expected Species'])
         _results.MLSTSpecies = str(r.loc[r.index[i], 'MLST Species'])
         _results.SequenceType = str(r.loc[r.index[i], 'Sequence Type'])
@@ -177,7 +180,7 @@
 
     #set the tree style
     ts = e.TreeStyle()
-    ts.show_leaf_name = False
+    ts.show_leaf_name = True
     ts.show_branch_length = True
     ts.scale = 2000 #pixel per branch length unit
     ts.branch_vertical_margin = 15 #pixel between branches
@@ -228,10 +231,13 @@
         elif (n.is_leaf() and not n.name == "Reference"): 
             #not reference branches, populate with metadata
             index = 0
-            mData = metadata[n.name.replace(".fa","")]
+            if (n.name.replace(".fa","") in metadata.keys()):
+                mData = metadata[n.name.replace(".fa","")]
+            else:
+                mData = metadata["na"]
             n.add_face(addFace(mData.ID), index, "aligned")
             index = index + 1
-            if (metadata[n.name.replace(".fa","")].new == True): #new column
+            if (mData.new == True): #new column
                 face = e.RectFace(30,30,"green","green") # TextFace("Y",fsize=10,tight_text=True)
                 face.border.margin = 5
                 face.margin_right = 5
@@ -271,4 +277,4 @@
 Main()
 
 end = time.time()
-print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
+print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
\ No newline at end of file

--- a/cpo_galaxy_tree.xml	Fri Aug 24 16:54:25 2018 -0400
+++ b/cpo_galaxy_tree.xml	Fri Aug 24 19:10:42 2018 -0400
@@ -5,7 +5,8 @@
     <requirement type="package" version="0.23.4">pandas</requirement>
     <requirement type="package" version="3.1.1">ete3</requirement>
     <requirement type="package" version="5.6.0">pyqt</requirement>
-   <requirement type="package" version="5.6.2">qt</requirement>
+	<requirement type="package" version="5.6.2">qt</requirement>
+
   </requirements>
 	<command detect_errors="exit_code">
     <![CDATA[
@@ -51,4 +52,4 @@
   url = {https://bfjia.net,
 }</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpo_galaxy_tree_sensitive.py	Fri Aug 24 19:10:42 2018 -0400
@@ -0,0 +1,397 @@
+#!/home/jjjjia/.conda/envs/py36/bin/python
+
+#$ -S /home/jjjjia/.conda/envs/py36/bin/python
+#$ -V             # Pass environment variables to the job
+#$ -N CPO_pipeline    # Replace with a more specific job name
+#$ -wd /home/jjjjia/testCases           # Use the current working dir
+#$ -pe smp 1      # Parallel Environment (how many cores)
+#$ -l h_vmem=11G  # Memory (RAM) allocation *per core*
+#$ -e ./logs/$JOB_ID.err
+#$ -o ./logs/$JOB_ID.log
+#$ -m ea
+#$ -M bja20@sfu.ca
+
+#   >python cpo_galaxy_tree.py -t /path/to/tree.ph -d /path/to/distance/matrix -m /path/to/metadata
+# python cpo_galaxy_tree.py -t tree.txt -d ./dist.tabular -m ./metadata.tsv
+
+#	<requirements>
+#		<requirement type="package" version="0.23.4">pandas</requirement>
+#		<requirement type="package" version="3.6">python</requirement>
+#       <requirement type="package" version="3.1.1">ete3</requirement>
+#		<requirement type="package" version="5.9.3">pyqt</requirement>
+#  </requirements>
+
+import subprocess
+import pandas #conda pandas
+import optparse
+import os
+import datetime
+import sys
+import time
+import urllib.request
+import gzip
+import collections
+import json
+import numpy #conda numpy
+import ete3 as e #conda ete3 3.1.1**** >requires pyqt5
+import csv 
+
+#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="identifier of the isolate")    
+parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/distance.tab", help="absolute file path forward read (R1)")
+parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tsv",help="absolute file path to reverse read (R2)")
+parser.add_option("-p", "--sensitive_data", dest="sensitivePath", type="string", default="", help="Spreadsheet (CSV) with sensitive metadata")
+parser.add_option("-c", "--sensitive_cols", dest="sensitiveCols", type="string", default="", help="CSV list of column names from sensitive metadata spreadsheet to use as labels on dendrogram")
+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.")
+parser.add_option("-b", "--bcid_column", dest="bcidCol", type="string", default="BCID", help="Column name of BCID in sensitive metadata file")
+parser.add_option("-n", "--missing_value", dest="naValue", type="string", default="NA", help="Value to write for missing data.")
+
+(options,args) = parser.parse_args()
+treePath = str(options.treePath).lstrip().rstrip()
+distancePath = str(options.distancePath).lstrip().rstrip()
+metadataPath = str(options.metadataPath).lstrip().rstrip()
+sensitivePath = str(options.sensitivePath).lstrip().rstrip()
+sensitiveCols = str(options.sensitiveCols).lstrip().rstrip()
+outputFile = str(options.outputFile).lstrip().rstrip()
+bcidCol = str( str(options.bcidCol).lstrip().rstrip() ) 
+naValue = str( str(options.naValue).lstrip().rstrip() ) 
+
+if len(sensitivePath) == 0:
+    print("Must give a file with sensitive meta data. Option -p, or --sensitive_data")
+    
+### test values to uncomment
+# sensitivePath = "./sensitive_metadata.csv"
+# sensitiveCols = "Name,Care facility"
+# outputFile = "newtree_test.png"
+# bcidCol = "BCID"
+
+
+
+import pandas
+class SensitiveMetadata(object):
+    def __init__(self):
+        x = pandas.read_csv( sensitivePath )
+        col_names = [ s for s in sensitiveCols.split(',')] # convert to 0 offset
+        if not bcidCol in col_names:
+            col_names.append( bcidCol )
+        all_cols = [ str(col) for col in x.columns ]
+        col_idxs = [ all_cols.index(col) for col in col_names ]
+        self.sensitive_data = x.iloc[:, col_idxs]
+    def get_columns(self):
+        cols = [ str(x) for x in self.sensitive_data.columns ]
+        return cols
+    def get_value( self, bcid, column_name ): # might be nice to get them all in single call via an input list of bcids ... for later
+        bcids= list( self.sensitive_data.loc[:, bcidCol ] ) # get the list of all BCIDs  in sensitive metadata
+        if not bcid in bcids:
+            return naValue
+        else:
+            row_idx = bcids.index( bcid )                        # lookup the row for this BCID
+        return self.sensitive_data.loc[ row_idx, column_name ]  # return the one value based on the column (col_idx) and this row
+
+
+#region result objects
+#define some objects to store values from results
+#//TODO this is not the proper way of get/set private object variables. every value has manually assigned defaults intead of specified in init(). Also, use property(def getVar, def setVar).
+class workflowResult(object):
+    def __init__(self):
+        self.new = False
+        self.ID	= "" 
+        self.ExpectedSpecies = ""
+        self.MLSTSpecies = ""
+        self.SequenceType = ""
+        self.MLSTScheme = ""
+        self.CarbapenemResistanceGenes =""
+        self.OtherAMRGenes=""
+        self.TotalPlasmids = 0
+        self.plasmids = []
+        self.DefinitelyPlasmidContigs =""
+        self.LikelyPlasmidContigs=""
+        self.row = ""
+class plasmidObj(object):
+    def __init__(self):
+        self.PlasmidsID = 0
+        self.Num_Contigs = 0
+        self.PlasmidLength	= 0
+        self.PlasmidRepType	= ""
+        self.PlasmidMobility = ""
+        self.NearestReference = ""
+
+#endregion
+
+#region useful functions
+def read(path): #read in a text file to a list
+    return [line.rstrip('\n') for line in open(path)]
+def execute(command): #subprocess.popen call bash command
+    process = subprocess.Popen(command, shell=False, cwd=curDir, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+
+    # Poll process for new output until finished
+    while True:
+        nextline = process.stdout.readline()
+        if nextline == '' and process.poll() is not None:
+            break
+        sys.stdout.write(nextline)
+        sys.stdout.flush()
+
+    output = process.communicate()[0]
+    exitCode = process.returncode
+
+    if (exitCode == 0):
+        return output
+    else:
+        raise subprocess.CalledProcessError(exitCode, command)
+def httpGetFile(url, filepath=""): #download a file from the web
+    if (filepath == ""):
+        return urllib.request.urlretrieve(url)
+    else:
+        urllib.request.urlretrieve(url, filepath)
+        return True
+def gunzip(inputpath="", outputpath=""): #gunzip
+    if (outputpath == ""):
+        with gzip.open(inputpath, 'rb') as f:
+            gzContent = f.read()
+        return gzContent
+    else:
+        with gzip.open(inputpath, 'rb') as f:
+            gzContent = f.read()
+        with open(outputpath, 'wb') as out:
+            out.write(gzContent)
+        return True
+def addFace(name): #function to add a facet to a tree
+    #if its the reference branch, populate the faces with column headers
+    face = e.faces.TextFace(name,fsize=10,tight_text=True)
+    face.border.margin = 5
+    face.margin_right = 5
+    face.margin_left = 5
+    return face
+#endregion
+
+#region functions to parse result files
+def ParseWorkflowResults(pathToResult):
+    _worflowResult = {}
+    r = pandas.read_csv(pathToResult, delimiter='\t', header=0) 
+    r = r.replace(numpy.nan, '', regex=True)
+    for i in range(len(r.index)):  
+        _results = workflowResult()
+        if(str(r.loc[r.index[i], 'new']).lower() == "new"):
+            _results.new = True
+        else:
+            _results.new = False        
+        _results.ID = str(r.loc[r.index[i], 'ID'])
+        _results.ExpectedSpecies = str(r.loc[r.index[i], 'Expected Species'])
+        _results.MLSTSpecies = str(r.loc[r.index[i], 'MLST Species'])
+        _results.SequenceType = str(r.loc[r.index[i], 'Sequence Type'])
+        _results.MLSTScheme = (str(r.loc[r.index[i], 'MLST Scheme']))
+        _results.CarbapenemResistanceGenes = (str(r.loc[r.index[i], 'Carbapenem Resistance Genes']))
+        _results.OtherAMRGenes = (str(r.loc[r.index[i], 'Other AMR Genes']))
+        _results.TotalPlasmids = int(r.loc[r.index[i], 'Total Plasmids'])
+        for j in range(0,_results.TotalPlasmids):
+            _plasmid = plasmidObj()
+            _plasmid.PlasmidsID =(((str(r.loc[r.index[i], 'Plasmids ID'])).split(";"))[j])
+            _plasmid.Num_Contigs = (((str(r.loc[r.index[i], 'Num_Contigs'])).split(";"))[j])
+            _plasmid.PlasmidLength	= (((str(r.loc[r.index[i], 'Plasmid Length'])).split(";"))[j])
+            _plasmid.PlasmidRepType	= (((str(r.loc[r.index[i], 'Plasmid RepType'])).split(";"))[j])
+            _plasmid.PlasmidMobility = ((str(r.loc[r.index[i], 'Plasmid Mobility'])).split(";"))[j]
+            _plasmid.NearestReference = ((str(r.loc[r.index[i], 'Nearest Reference'])).split(";"))[j]
+            _results.plasmids.append(_plasmid)
+        _results.DefinitelyPlasmidContigs = (str(r.loc[r.index[i], 'Definitely Plasmid Contigs']))
+        _results.LikelyPlasmidContigs = (str(r.loc[r.index[i], 'Likely Plasmid Contigs']))
+        _results.row = "\t".join(str(x) for x in r.ix[i].tolist())
+        _worflowResult[_results.ID] = _results
+    return _worflowResult
+
+#endregion
+
+def Main():
+    sensitive_meta_data = SensitiveMetadata()
+    # print( sensitive_meta_data.get_columns() )
+    metadata = ParseWorkflowResults(metadataPath)
+    distance = read(distancePath)
+    treeFile = "".join(read(treePath))
+
+    distanceDict = {} #store the distance matrix as rowname:list<string>
+    for i in range(len(distance)):
+        temp = distance[i].split("\t")
+        distanceDict[temp[0]] = temp[1:]
+    #region step5: tree construction
+
+    '''
+    #region create detailed tree
+    
+    plasmidCount = 0
+    for n in t.traverse():
+        if (n.is_leaf() and not n.name == "Reference"):
+            mData = metadata[n.name.replace(".fa","")]
+            face = faces.TextFace(mData.MLSTSpecies,fsize=10,tight_text=True)
+            face.border.margin = 5
+            face.margin_left = 10
+            face.margin_right = 10
+            n.add_face(face, 0, "aligned")
+            face = faces.TextFace(mData.SequenceType,fsize=10,tight_text=True)
+            face.border.margin = 5
+            face.margin_right = 10
+            n.add_face(face, 1, "aligned")
+            face = faces.TextFace(mData.CarbapenemResistanceGenes,fsize=10,tight_text=True)
+            face.border.margin = 5
+            face.margin_right = 10
+            n.add_face(face, 2, "aligned")
+            index = 3
+            if (mData.TotalPlasmids > plasmidCount):
+                plasmidCount = mData.TotalPlasmids
+            for i in range(0, mData.TotalPlasmids):
+                face = faces.TextFace(mData.plasmids[i].PlasmidRepType,fsize=10,tight_text=True)
+                face.border.margin = 5
+                face.margin_right = 10
+                n.add_face(face, index, "aligned")
+                index+=1
+                face = faces.TextFace(mData.plasmids[i].PlasmidMobility,fsize=10,tight_text=True)
+                face.border.margin = 5
+                face.margin_right = 10
+                n.add_face(face, index, "aligned")
+                index+=1
+
+    face = faces.TextFace("Species",fsize=10,tight_text=True)
+    face.border.margin = 5
+    face.margin_right = 10
+    face.margin_left = 10
+    (t&"Reference").add_face(face, 0, "aligned")
+    face = faces.TextFace("Sequence Type",fsize=10,tight_text=True)
+    face.border.margin = 5
+    face.margin_right = 10
+    (t&"Reference").add_face(face, 1, "aligned")
+    face = faces.TextFace("Carbapenamases",fsize=10,tight_text=True)
+    face.border.margin = 5
+    face.margin_right = 10
+    (t&"Reference").add_face(face, 2, "aligned")
+    index = 3
+    for i in range(0, plasmidCount):
+        face = faces.TextFace("plasmid " + str(i) + " replicons",fsize=10,tight_text=True)
+        face.border.margin = 5
+        face.margin_right = 10
+        (t&"Reference").add_face(face, index, "aligned")
+        index+=1
+        face = faces.TextFace("plasmid " + str(i) + " mobility",fsize=10,tight_text=True)
+        face.border.margin = 5
+        face.margin_right = 10
+        (t&"Reference").add_face(face, index, "aligned")
+        index+=1
+
+    t.render("./pipelineTest/tree.png", w=5000,units="mm", tree_style=ts)
+    
+    #endregion
+    '''
+    #region create box tree
+    #region step5: tree construction
+    treeFile = "".join(read(treePath))
+    t = e.Tree(treeFile)
+    t.set_outgroup(t&"Reference")
+
+    #set the tree style
+    ts = e.TreeStyle()
+    ts.show_leaf_name = False
+    ts.show_branch_length = True
+    ts.scale = 2000 #pixel per branch length unit
+    ts.branch_vertical_margin = 15 #pixel between branches
+    style2 = e.NodeStyle()
+    style2["fgcolor"] = "#000000"
+    style2["shape"] = "circle"
+    style2["vt_line_color"] = "#0000aa"
+    style2["hz_line_color"] = "#0000aa"
+    style2["vt_line_width"] = 2
+    style2["hz_line_width"] = 2
+    style2["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
+    style2["hz_line_type"] = 0
+    for n in t.traverse():
+        n.set_style(style2)
+
+    #find the plasmid origins
+    plasmidIncs = {}
+    for key in metadata:
+        for plasmid in metadata[key].plasmids:
+            for inc in plasmid.PlasmidRepType.split(","):
+                if (inc.lower().find("inc") > -1):
+                    if not (inc in plasmidIncs):
+                        plasmidIncs[inc] = [metadata[key].ID]
+                    else:
+                        if metadata[key].ID not in plasmidIncs[inc]:
+                            plasmidIncs[inc].append(metadata[key].ID)
+    #plasmidIncs = sorted(plasmidIncs)
+    for n in t.traverse(): #loop through the nodes of a tree
+        if (n.is_leaf() and n.name == "Reference"):
+            #if its the reference branch, populate the faces with column headers
+            index = 0
+            
+            for sensitive_data_column in sensitive_meta_data.get_columns():
+                (t&"Reference").add_face(addFace(sensitive_data_column), index, "aligned")
+                index = index + 1
+            
+            (t&"Reference").add_face(addFace("SampleID"), index, "aligned")
+            index = index + 1
+            (t&"Reference").add_face(addFace("New?"), index, "aligned")
+            index = index + 1
+            for i in range(len(plasmidIncs)): #this loop adds the columns (aka the incs) to the reference node
+                (t&"Reference").add_face(addFace(list(plasmidIncs.keys())[i]), i + index, "aligned")
+            index = index + len(plasmidIncs)
+            (t&"Reference").add_face(addFace("MLSTScheme"), index, "aligned")
+            index = index + 1
+            (t&"Reference").add_face(addFace("Sequence Type"), index, "aligned")
+            index = index + 1 
+            (t&"Reference").add_face(addFace("Carbapenamases"), index, "aligned")
+            index = index + 1
+            for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds the distance matrix
+                (t&"Reference").add_face(addFace(distanceDict[list(distanceDict.keys())[0]][i]), index + i, "aligned")
+            index = index + len(distanceDict[list(distanceDict.keys())[0]])
+        elif (n.is_leaf() and not n.name == "Reference"): 
+            #not reference branches, populate with metadata
+            index = 0
+            mData = metadata[n.name.replace(".fa","")]
+
+            # pushing in sensitive data
+            for sensitive_data_column in sensitive_meta_data.get_columns():
+                sens_col_val = sensitive_meta_data.get_value(bcid=mData.ID, column_name=sensitive_data_column )
+                n.add_face(addFace(sens_col_val), index, "aligned")
+                index = index + 1
+
+            n.add_face(addFace(mData.ID), index, "aligned")
+            index = index + 1
+            if (metadata[n.name.replace(".fa","")].new == True): #new column
+                face = e.RectFace(30,30,"green","green") # TextFace("Y",fsize=10,tight_text=True)
+                face.border.margin = 5
+                face.margin_right = 5
+                face.margin_left = 5
+                face.vt_align = 1
+                face.ht_align = 1
+                n.add_face(face, index, "aligned")
+            index = index + 1
+            for incs in plasmidIncs: #this loop adds presence/absence to the sample nodes
+                if (n.name.replace(".fa","") in plasmidIncs[incs]):
+                    face = e.RectFace(30,30,"black","black") # TextFace("Y",fsize=10,tight_text=True)
+                    face.border.margin = 5
+                    face.margin_right = 5
+                    face.margin_left = 5
+                    face.vt_align = 1
+                    face.ht_align = 1
+                    n.add_face(face, list(plasmidIncs.keys()).index(incs) + index, "aligned")
+            index = index + len(plasmidIncs)
+            n.add_face(addFace(mData.MLSTSpecies), index, "aligned")
+            index = index + 1
+            n.add_face(addFace(mData.SequenceType), index, "aligned")
+            index = index + 1
+            n.add_face(addFace(mData.CarbapenemResistanceGenes), index, "aligned")
+            index = index + 1
+            for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds distance matrix
+                n.add_face(addFace(list(distanceDict[n.name])[i]), index + i, "aligned")
+                
+    t.render( outputFile, w=5000,units="mm", tree_style=ts) #save it as a png. or an phyloxml
+
+    #endregion
+#endregion
+
+
+start = time.time()#time the analysis
+
+#analysis time
+Main()
+
+end = time.time()
+print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
\ No newline at end of file

--- a/cpo_snippy.xml	Fri Aug 24 16:54:25 2018 -0400
+++ b/cpo_snippy.xml	Fri Aug 24 19:10:42 2018 -0400
@@ -34,7 +34,7 @@
       &&
 
       #import re
-      #set $dir_name = re.sub('[^\w_]', '_', $input.element_identifier)
+      #set $dir_name = ($input.element_identifier)
       mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
 
       tar -czf out.tgz ${dir_name}