# HG changeset patch
# User yating-l
# Date 1471040819 14400
# Node ID 211c9b3a5c1526d587811c3621c8cad235c219fb
# Parent  04e57f9ef873b7834d9e499e9f6cc60154c9d6f6
planemo upload commit 6e3286c6569d531846474dcd6959378af0317ce3-dirty

diff -r 04e57f9ef873 -r 211c9b3a5c15 Group.pyc
Binary file Group.pyc has changed
diff -r 04e57f9ef873 -r 211c9b3a5c15 error.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/error.txt	Fri Aug 12 18:26:59 2016 -0400
@@ -0,0 +1,2 @@
+scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
+scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
diff -r 04e57f9ef873 -r 211c9b3a5c15 gff2Togff3.py
--- a/gff2Togff3.py	Fri Aug 12 15:01:58 2016 -0400
+++ b/gff2Togff3.py	Fri Aug 12 18:26:59 2016 -0400
@@ -1,10 +1,28 @@
-
+import argparse
+import sys
+import fileinput
 from Group import Group
 
-class Convertor:
+def main():
+        parser = argparse.ArgumentParser(description='Get a gff file and the output gff3 file')
+        parser.add_argument('--input', help='input gff file')
+        parser.add_argument('--output', help='output gff3 file', required=True)
+        args = parser.parse_args()
+        input = args.input
+        output = args.output
+        if not sys.stdin.isatty():
+            c = Convertor(sys.stdin, output)
+        else: 
+            c = Convertor(input, output)
+        c.convert()
+        
+class Convertor:    
     def __init__(self, input, output):
-        with open(input) as self.f:
-            self.li = [line.rstrip().split("\t") for line in self.f]
+        if type(input) is str:
+            with open(input) as self.f:
+                self.li = [line.rstrip().split("\t") for line in self.f]
+        else:
+            self.li = [line.rstrip().split("\t") for line in input]
         self.gff3 = open(output, "w")
         self.gff3.write("##gff-version 3\n")
 
@@ -35,8 +53,7 @@
         
 
 if __name__ == "__main__":
-    file = Convertor("dbia3.gff", "test.txt")
-    file.convert()
+    main()
 
 
     
\ No newline at end of file
diff -r 04e57f9ef873 -r 211c9b3a5c15 out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out	Fri Aug 12 18:26:59 2016 -0400
@@ -0,0 +1,2 @@
+scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
+scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done
diff -r 04e57f9ef873 -r 211c9b3a5c15 snap.xml
--- a/snap.xml	Fri Aug 12 15:01:58 2016 -0400
+++ b/snap.xml	Fri Aug 12 18:26:59 2016 -0400
@@ -20,11 +20,10 @@
         $transcripts "$output3"
         #end if
         -gff
+        -quiet
         $organism
-        from gff2Togff3 import Convertor
-        f = Convertor("$output1", "$output4")
-        f.convert()
-        "$input1" > "$output4"
+        $input1
+        | python $__tool_directory__/gff2Togff3.py --output $output1
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="dna.gz" />
@@ -89,7 +88,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="gff" label="${tool.name} on ${on_string}: GTF/GFF">
+        <data name="output1" format="gff3" label="${tool.name} on ${on_string}: GTF/GFF3">
         </data>
         <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
             <filter>proteins == "-aa"</filter>
@@ -102,8 +101,7 @@
         <test>
             <param name="input1" value="thale.dna.gz"/>
             <param name="organism" value="At.hmm" />
-            <param name="format" value="-gff" />
-            <output name="output1" file="thale.gff"/>
+            <output name="output1" file="thale.gff3"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 04e57f9ef873 -r 211c9b3a5c15 test.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.txt	Fri Aug 12 18:26:59 2016 -0400
@@ -0,0 +1,27 @@
+##gff-version 3
+At1g01040.0	SNAP	gene	1007	5917	.	+	.	ID=At1g01040.0-snap.1
+At1g01040.0	SNAP	mRNA	1007	5917	.	+	.	ID=mRNA_At1g01040.0-snap.1;Parent=At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	1007	1954	85.269	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	2024	2137	8.926	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	2234	2444	20.788	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	2523	2917	35.162	+	2	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3006	3225	34.428	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3307	3479	14.790	+	2	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3563	3685	4.678	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3774	3934	10.179	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4025	4258	25.991	+	1	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4344	4506	4.289	+	1	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4581	4763	28.696	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4854	5015	15.217	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	5100	5195	23.205	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	5285	5917	45.878	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	gene	6086	8561	.	+	.	ID=At1g01040.0-snap.2
+At1g01040.0	SNAP	mRNA	6086	8561	.	+	.	ID=mRNA_At1g01040.0-snap.2;Parent=At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6086	6144	6.596	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6190	6287	22.495	+	1	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6372	6562	17.809	+	2	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6642	6803	16.407	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6828	7547	69.159	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	7629	7793	40.262	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	7892	8298	46.310	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	8384	8561	17.079	+	1	Parent=mRNA_At1g01040.0-snap.2