# HG changeset patch
# User jowong
# Date 1542129593 18000
# Node ID 63f3743c2ae4736aad57479a6af999d0e5d7f253
# Parent  0032da940600bd7db97e87481533a54a97ef82ad
planemo upload

diff -r 0032da940600 -r 63f3743c2ae4 filler.py
--- a/filler.py	Mon Oct 29 08:30:06 2018 -0400
+++ b/filler.py	Tue Nov 13 12:19:53 2018 -0500
@@ -7,7 +7,7 @@
                            description="produce filler collection to deal with galaxy handling")
 
 input = parser.add_argument_group('Input', '')
-input.add_argument('-i', '--input', nargs=1, required=True, help="Paths to forward reads")
+input.add_argument('-i', '--input', nargs=1, required=True, help="Paths to (forward) reads")
 input.add_argument('-o', '--output', nargs=1, required=True, help="output")
 
 if len(sys.argv) == 0:
diff -r 0032da940600 -r 63f3743c2ae4 filler.xml
--- a/filler.xml	Mon Oct 29 08:30:06 2018 -0400
+++ b/filler.xml	Tue Nov 13 12:19:53 2018 -0500
@@ -1,12 +1,12 @@
-<tool id="filler" name="Filler" version="1.0.0">
+<tool id="filler" name="Filler" version="1.0.1">
     <description>Filler Function to deal with paired collection</description>
     <command interpreter="python"><![CDATA[
       filler.py 
         #if str( $data_input.data_selector ) == "paired"       
-          -i $data_input.input1.forward.element_identifier      
+          -i $data_input.input1.forward      
         #end if
         #if str( $data_input.data_selector ) == "single"       
-          -i "$data_input.input2.element_identifier"
+          -i "$data_input.input2"
         #end if
         
         -o $output
diff -r 0032da940600 -r 63f3743c2ae4 prince.xml
--- a/prince.xml	Mon Oct 29 08:30:06 2018 -0400
+++ b/prince.xml	Tue Nov 13 12:19:53 2018 -0500
@@ -1,7 +1,7 @@
-<tool id="prince" name="VNTR copy number approximation" version="1.0.1">
+<tool id="prince" name="VNTR copy number approximation" version="1.1.0">
     <description>Calculates CNV of genomic data based on template</description>
     <requirements>
-        <requirement type="package" version="1.0">prince</requirement>
+        <requirement type="package" version="1.2">prince</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         prince -tf "$input1" -to "$output1"
diff -r 0032da940600 -r 63f3743c2ae4 prince_postprocess.py
--- a/prince_postprocess.py	Mon Oct 29 08:30:06 2018 -0400
+++ b/prince_postprocess.py	Tue Nov 13 12:19:53 2018 -0500
@@ -8,8 +8,8 @@
 
 input = parser.add_argument_group('Input', '')
 input.add_argument('-i', '--input', nargs=1, required=True, help="PRINCE OUTPUT")
-input.add_argument('-s', '--sample', nargs='*', required=True, help="Sample names")
-
+input.add_argument('-s', '--sample', nargs='+', required=True, help="Sample names")
+input.add_argument('-f', '--file', nargs='+', required=True, help="File of forward reads in galaxy convention")
 if len(sys.argv) == 0:
     parser.print_usage()
     sys.exit(1)
@@ -18,6 +18,19 @@
 
 #print(args.input)
 #sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.label.rstrip().lstrip())
+sample_dict={}
+path_index = 0
+for path in args.file:
+	with open(path) as f:
+		for line in f:
+			sample_dict[re.sub(".*/","",line)] = sample[path_index]
+	path_index += 1
+			
+			
+
+
+
+
 
 with open(args.input[0]) as prince_output:
 	with open('prince_postprocess_output.txt', 'w') as output:
@@ -25,8 +38,9 @@
 		index = 0
 		for line in prince_output:
 			if x%2 == 0:
-                                sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index])
-				output.write(re.sub('.*.dat', sample, line))
+				entries =line.rstrip().split(',')
+                                sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', sample_dict[entries[0]])
+				output.write(re.sub(entries[0], sample, line))
 				index += 1
 			else:
 				output.write(line)
diff -r 0032da940600 -r 63f3743c2ae4 prince_postprocess.xml
--- a/prince_postprocess.xml	Mon Oct 29 08:30:06 2018 -0400
+++ b/prince_postprocess.xml	Tue Nov 13 12:19:53 2018 -0500
@@ -1,7 +1,7 @@
 <tool id="prince_postprocess" name="Prince Postprocess" version="1.0.0">
     <description>Postprocess PRINCE galaxy output</description>
     <command interpreter="python"><![CDATA[
-        prince_postprocess.py -i $prince_output  -s #for $path in $paths# $path.element_identifier #end for#
+        prince_postprocess.py -i $prince_output  -s #for $path in $paths# $path.element_identifier #end for# -f #for $path in $paths# $path #end for#
     ]]></command>
     <inputs>
         <param name="paths" type="data" format="data" label="Collection of files" help="" optional="False" multiple="True"/>