# HG changeset patch
# User mvdbeek
# Date 1534789669 14400
# Node ID 21b5a9170b9008e98e1f939057a1c8e6daeca899
# Parent  c8c7b6113241b61ef6fb04dd4abd827098e38720
planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit c8e0a703fcdff580ba0a0c5806a37c088c03ab7b

diff -r c8c7b6113241 -r 21b5a9170b90 alignment_size_distribution.xml
--- a/alignment_size_distribution.xml	Mon Aug 20 13:02:42 2018 -0400
+++ b/alignment_size_distribution.xml	Mon Aug 20 14:27:49 2018 -0400
@@ -10,7 +10,7 @@
     <inputs>
         <param name="alignment_file" type="data" format="bam,unsorted.bam"/>
         <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/>
-        <param argument="--maximum_size" type="integer" value="18" min="1" label="Maximum read length to consider"/>
+        <param argument="--maximum_size" type="integer" value="30" min="1" label="Maximum read length to consider"/>
         <param argument="--wide" type="boolean" checked="false" truevalue="--wide" falsevalue="--long" label="Output wide instead of long tabular format"/>
     </inputs>
     <outputs>
diff -r c8c7b6113241 -r 21b5a9170b90 size_distributions.py
--- a/size_distributions.py	Mon Aug 20 13:02:42 2018 -0400
+++ b/size_distributions.py	Mon Aug 20 14:27:49 2018 -0400
@@ -40,7 +40,7 @@
 
 
 def write_table(df, output_path):
-    df.to_csv(output_path, sep="\t")
+    df.to_csv(output_path, sep="\t", index=False)
 
 
 @click.command()
diff -r c8c7b6113241 -r 21b5a9170b90 test-data/distribution.tab
--- a/test-data/distribution.tab	Mon Aug 20 13:02:42 2018 -0400
+++ b/test-data/distribution.tab	Mon Aug 20 14:27:49 2018 -0400
@@ -1,27 +1,27 @@
-readlength	orientation	FBgn0026065_Idefix
-18	antisense	6
-18	sense	3
-19	antisense	7
-19	sense	1
-20	antisense	6
-20	sense	4
-21	antisense	6
-21	sense	6
-22	antisense	5
-22	sense	2
-23	antisense	5
-23	sense	2
-24	antisense	2
-24	sense	3
-25	antisense	3
-25	sense	0
-26	antisense	3
-26	sense	4
-27	antisense	6
-27	sense	3
-28	antisense	2
-28	sense	2
-29	antisense	0
-29	sense	3
-30	antisense	0
-30	sense	1
+readlength	orientation	reference	count
+18	sense	FBgn0026065_Idefix	3
+18	antisense	FBgn0026065_Idefix	6
+19	sense	FBgn0026065_Idefix	1
+19	antisense	FBgn0026065_Idefix	7
+20	sense	FBgn0026065_Idefix	4
+20	antisense	FBgn0026065_Idefix	6
+21	sense	FBgn0026065_Idefix	6
+21	antisense	FBgn0026065_Idefix	6
+22	sense	FBgn0026065_Idefix	2
+22	antisense	FBgn0026065_Idefix	5
+23	sense	FBgn0026065_Idefix	2
+23	antisense	FBgn0026065_Idefix	5
+24	sense	FBgn0026065_Idefix	3
+24	antisense	FBgn0026065_Idefix	2
+25	sense	FBgn0026065_Idefix	0
+25	antisense	FBgn0026065_Idefix	3
+26	sense	FBgn0026065_Idefix	4
+26	antisense	FBgn0026065_Idefix	3
+27	sense	FBgn0026065_Idefix	3
+27	antisense	FBgn0026065_Idefix	6
+28	sense	FBgn0026065_Idefix	2
+28	antisense	FBgn0026065_Idefix	2
+29	sense	FBgn0026065_Idefix	3
+29	antisense	FBgn0026065_Idefix	0
+30	sense	FBgn0026065_Idefix	1
+30	antisense	FBgn0026065_Idefix	0