# HG changeset patch
# User mheinzl
# Date 1565800695 14400
# Node ID f72593bcc8ee3d0340f257850736e0d5c0bed33f
# Parent  321a4871564bc060048d2565e6e2f5ecd257c18a
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty

diff -r 321a4871564b -r f72593bcc8ee fsd.py
--- a/fsd.py	Wed Aug 14 08:29:27 2019 -0400
+++ b/fsd.py	Wed Aug 14 12:38:15 2019 -0400
@@ -557,6 +557,9 @@
             output_file.write("absolute frequency:{}{}\n".format(sep, count[len(count) - 1]))
             output_file.write("relative frequency:{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count)))
 
+            output_file.write("median family size:{}{}\n".format(sep, numpy.median(numpy.array(integers))))
+            output_file.write("mean family size:{}{}\n\n".format(sep, numpy.mean(numpy.array(integers))))
+
             output_file.write("{}singletons:{}{}{}family size > 20:{}{}{}{}length of dataset:\n".format(sep, sep, sep, sep, sep, sep, sep, sep))
             output_file.write("{}nr. of tags{}rel. freq of tags{}rel.freq of PE reads{}nr. of tags{}rel. freq of tags{}nr. of PE reads{}rel. freq of PE reads{}total nr. of tags{}total nr. of PE reads\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep))
             output_file.write("{}{}{}{}{:.3f}{}{:.3f}{}{}{}{:.3f}{}{}{}{:.3f}{}{}{}{}\n\n".format(
diff -r 321a4871564b -r f72593bcc8ee fsd.xml
--- a/fsd.xml	Wed Aug 14 08:29:27 2019 -0400
+++ b/fsd.xml	Wed Aug 14 12:38:15 2019 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- galaxy version 16.04 -->
-<tool id="fsd" name="FSD" version="1.0.3">
+<tool id="fsd" name="FSD" version="1.0.4">
     <description>: Family Size Distribution of duplex sequencing tags</description>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
diff -r 321a4871564b -r f72593bcc8ee test-data/fsd_output1.tab
--- a/test-data/fsd_output1.tab	Wed Aug 14 08:29:27 2019 -0400
+++ b/test-data/fsd_output1.tab	Wed Aug 14 12:38:15 2019 -0400
@@ -55,6 +55,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data1.tab	63	0.562	0.167	1	0.009	21	0.056	112	378
@@ -105,6 +108,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data2.tab	63	0.562	0.167	1	0.009	21	0.056	112	378
@@ -155,6 +161,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data3.tab	63	0.562	0.167	1	0.009	21	0.056	112	378
@@ -205,6 +214,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data4.tab	63	0.562	0.167	1	0.009	21	0.056	112	378
diff -r 321a4871564b -r f72593bcc8ee test-data/fsd_output2.tab
--- a/test-data/fsd_output2.tab	Wed Aug 14 08:29:27 2019 -0400
+++ b/test-data/fsd_output2.tab	Wed Aug 14 12:38:15 2019 -0400
@@ -55,6 +55,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data1.tab	63	0.562	0.167	1	0.009	21	0.056	112	378
@@ -105,6 +108,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data2.tab	63	0.562	0.167	1	0.009	21	0.056	112	378
@@ -155,6 +161,9 @@
 absolute frequency:	1
 relative frequency:	0.009
 
+median family size:	1.0
+mean family size:	3.375
+
 	singletons:			family size > 20:				length of dataset:
 	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
 fsd_data3.tab	63	0.562	0.167	1	0.009	21	0.056	112	378