# HG changeset patch
# User iuc
# Date 1607014763 0
# Node ID 4a7f4b0cc0a3691319996e8c8822e0f3e7915e25
# Parent  965674d88d34f0265cc23697a8ef6fcac8388f70
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"

diff -r 965674d88d34 -r 4a7f4b0cc0a3 tbl2gff3.py
--- a/tbl2gff3.py	Tue Jul 07 04:20:40 2020 -0400
+++ b/tbl2gff3.py	Thu Dec 03 16:59:23 2020 +0000
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 import argparse
+import collections
 import csv
 import sys
 
@@ -32,9 +33,10 @@
     a=None,
     strand_column=None,
     strand_value=None,
+    strand_infer=False,
 ):
 
-    records = {}
+    records = collections.OrderedDict()
 
     for row in csv.reader(table, delimiter="\t"):
         # print(', '.join(row))
@@ -51,22 +53,34 @@
 
         q["source"] = c(row, source, "tbl2gff3")
 
+        begin_i = int(c(row, begin))
+        end_i = int(c(row, end))
+
+        begin_f = min(begin_i, end_i)
+        end_f = max(begin_i, end_i)
+
         _str = None
         if strand_column is not None:
             _str = int(c(row, strand_column))
         elif strand_value is not None:
             _str = int(strand_value)
+        if strand_infer:
+            if begin_i > begin_f:
+                _str = -1
+            else:
+                _str = 1
 
-        for x in a:
-            k, v = x.split(":", 1)
-            _v = c(row, v)
-            if k in q:
-                q[k].append(_v)
-            else:
-                q[k] = [_v]
+        if a is not None:
+            for x in a:
+                k, v = x.split(":", 1)
+                _v = c(row, v)
+                if k in q:
+                    q[k].append(_v)
+                else:
+                    q[k] = [_v]
 
         f = SeqFeature(
-            FeatureLocation(int(c(row, begin)), int(c(row, end))),
+            FeatureLocation(begin_f, end_f),
             type=c(row, type),
             strand=_str,
             qualifiers=q,
@@ -85,6 +99,7 @@
     parser.add_argument("--type", help="feature type column")
     parser.add_argument("--score", help="score column")
     parser.add_argument("--source", help="source column")
+    parser.add_argument("--strand_infer", action='store_true', help="infer strand")
     parser.add_argument("--strand_column", help="strand column")
     parser.add_argument("--strand_value", help="strand value")
     # parser.add_argument('--frame', help='frame column')
diff -r 965674d88d34 -r 4a7f4b0cc0a3 tbl2gff3.xml
--- a/tbl2gff3.xml	Tue Jul 07 04:20:40 2020 -0400
+++ b/tbl2gff3.xml	Thu Dec 03 16:59:23 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="tbl2gff3" name="Table to GFF3" version="1.1">
+<tool id="tbl2gff3" name="Table to GFF3" version="1.2">
 	<description></description>
 	<macros>
 		<import>macros.xml</import>
@@ -24,7 +24,9 @@
 				--source '$source'
 			#end if
 
-			#if str($strand.strand_select) != "none":
+			#if str($strand.strand_select) == 'infer':
+				--strand_infer
+			#else if str($strand.strand_select) != "none":
 				--strand_${strand.strand_select} '${strand.strand}'
 			#end if
 
@@ -38,20 +40,22 @@
 		<param label="Table" name="table" type="data" format="tabular"/>
 
 		<param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/>
-		<param name="begin" type="text" value="" optional="false" label="Feature start column or value" help="@HELP@"/>
-		<param name="end" type="text" value="" optional="false" label="Feature end column or value" help="@HELP@"/>
-		<param name="type" type="text" value="sequence_feature" label="Feature type column or value" help="@HELP@"/>
-		<param name="score" type="text" value="" label="Feature score column or value" help="@HELP@"/>
-		<param name="source" type="text" value="tbl2gff3" label="Feature source column or value" help="@HELP@"/>
+		<param name="begin" type="text" value="" optional="false" label="Start column or value" help="@HELP@"/>
+		<param name="end" type="text" value="" optional="false" label="End column or value" help="@HELP@"/>
+		<param name="type" type="text" value="sequence_feature" label="Type column or value" help="@HELP@"/>
+		<param name="score" type="text" value="" label="Score column or value" help="@HELP@"/>
+		<param name="source" type="text" value="tbl2gff3" label="Source column or value" help="@HELP@"/>
 
 
 		<conditional name="strand">
 			<param name="strand_select" type="select" label="Strand">
+				<option value="infer">Infer</option>
 				<option value="none">Not specified</option>
 				<option value="column">From Column</option>
 				<option value="value">Specify Value</option>
 			</param>
 			<when value="none" />
+			<when value="infer" />
 			<when value="column" >
 				<param name="strand" type="text" value="" label="Strand column" />
 			</when>
@@ -104,6 +108,17 @@
 			<output name="output" file="blast.gff3" />
 
 		</test>
+		<test>
+			<param name="table" ftype="tabular" value="infer.tab" />
+			<param name="rid" value="1" />
+			<param name="begin" value="2" />
+			<param name="end" value="3" />
+			<conditional name="strand">
+				<param name="strand_select" value="infer"/>
+			</conditional>
+			<output name="output" file="infer.gff3" />
+
+		</test>
 	</tests>
 	<help><![CDATA[
 **What it does**
diff -r 965674d88d34 -r 4a7f4b0cc0a3 test-data/infer.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/infer.gff3	Thu Dec 03 16:59:23 2020 +0000
@@ -0,0 +1,6 @@
+##gff-version 3
+##sequence-region a 1 4
+a	tbl2gff3	sequence_feature	101	200	.	+	.	
+##gff-version 3
+##sequence-region b 1 4
+b	tbl2gff3	sequence_feature	101	200	.	-	.	
diff -r 965674d88d34 -r 4a7f4b0cc0a3 test-data/infer.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/infer.tab	Thu Dec 03 16:59:23 2020 +0000
@@ -0,0 +1,2 @@
+a	100	200
+b	200	100