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changeset 44:a76af7fd9fca draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty
author mheinzl
date Wed, 14 Aug 2019 13:03:14 -0400
parents f72593bcc8ee
children 6651e76baca1
files fsd.py fsd.xml
diffstat 2 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/fsd.py	Wed Aug 14 12:38:15 2019 -0400
+++ b/fsd.py	Wed Aug 14 13:03:14 2019 -0400
@@ -551,14 +551,14 @@
             plt.close()
 
             # write same information to a csv file
-            count = numpy.bincount(integers)  # original counts of family sizes
+            count = numpy.bincount(data_o)  # original counts of family sizes
             output_file.write("\nDataset:{}{}\n".format(sep, name_file))
-            output_file.write("max. family size:{}{}\n".format(sep, max(integers)))
+            output_file.write("max. family size:{}{}\n".format(sep, max(data_o)))
             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("median family size:{}{}\n".format(sep, numpy.median(numpy.array(data_o))))
+            output_file.write("mean family size:{}{}\n\n".format(sep, numpy.mean(numpy.array(data_o))))
 
             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))
--- a/fsd.xml	Wed Aug 14 12:38:15 2019 -0400
+++ b/fsd.xml	Wed Aug 14 13:03:14 2019 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- galaxy version 16.04 -->
-<tool id="fsd" name="FSD" version="1.0.4">
+<tool id="fsd" name="FSD" version="1.0.5">
     <description>: Family Size Distribution of duplex sequencing tags</description>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>