# HG changeset patch
# User iuc
# Date 1469527577 14400
# Node ID abc464ca7260dc385840f795c2e403131d426774
# Parent d4db13c9dd7f29596688249216c34d3deb4c057b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1
diff -r d4db13c9dd7f -r abc464ca7260 cwpair2.xml
--- a/cwpair2.xml Wed Dec 23 09:26:01 2015 -0500
+++ b/cwpair2.xml Tue Jul 26 06:06:17 2016 -0400
@@ -85,9 +85,9 @@
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@@ -101,26 +101,26 @@
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diff -r d4db13c9dd7f -r abc464ca7260 cwpair2_util.py
--- a/cwpair2_util.py Wed Dec 23 09:26:01 2015 -0500
+++ b/cwpair2_util.py Tue Jul 26 06:06:17 2016 -0400
@@ -3,9 +3,10 @@
import os
import sys
import traceback
+
import matplotlib
matplotlib.use('Agg')
-from matplotlib import pyplot
+from matplotlib import pyplot # noqa: E402
# Data outputs
DETAILS = 'D'
@@ -47,7 +48,7 @@
"""
Returns the bin in which a data point falls
"""
- return self.start + (x-self.start) // self.binsize * self.binsize + self.binsize/2.0
+ return self.start + (x - self.start) // self.binsize * self.binsize + self.binsize / 2.0
def add(self, x):
x = self.get_bin(x)
@@ -75,7 +76,7 @@
def distance(peak1, peak2):
- return (peak2[1]+peak2[2])/2 - (peak1[1]+peak1[2])/2
+ return (peak2[1] + peak2[2]) / 2 - (peak1[1] + peak1[2]) / 2
def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}):
@@ -114,7 +115,7 @@
values.append(peak[3])
values.sort()
# Get 95% value
- return values[int(len(values)*0.95)]
+ return values[int(len(values) * 0.95)]
def filter(chromosomes, threshold=0.05):
@@ -149,7 +150,7 @@
def make_keys(crick):
- return [(data[1] + data[2])//2 for data in crick]
+ return [(data[1] + data[2]) // 2 for data in crick]
def get_window(crick, peak, up_distance, down_distance, keys=None):
@@ -190,7 +191,7 @@
def match_mode(window, peak, mode):
if not window:
return None
- return min(window, key=lambda cpeak: abs(distance(peak, cpeak)-mode))
+ return min(window, key=lambda cpeak: abs(distance(peak, cpeak) - mode))
METHODS = {'mode': match_mode, 'closest': match_closest, 'largest': match_largest}
@@ -351,9 +352,9 @@
match[2],
match[3], '-',
midpoint,
- peak[3]+match[3],
+ peak[3] + match[3],
d))
- i = bisect.bisect_left(keys, (match[1]+match[2])/2)
+ i = bisect.bisect_left(keys, (match[1] + match[2]) / 2)
del crick[i]
del keys[i]
else:
diff -r d4db13c9dd7f -r abc464ca7260 cwpair2_util.pyc
Binary file cwpair2_util.pyc has changed
diff -r d4db13c9dd7f -r abc464ca7260 test-data/closest_f_output2.pdf
Binary file test-data/closest_f_output2.pdf has changed
diff -r d4db13c9dd7f -r abc464ca7260 test-data/largest_f_output2.pdf
Binary file test-data/largest_f_output2.pdf has changed
diff -r d4db13c9dd7f -r abc464ca7260 test-data/magic.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/magic.pdf Tue Jul 26 06:06:17 2016 -0400
@@ -0,0 +1,1 @@
+%PDF-
diff -r d4db13c9dd7f -r abc464ca7260 test-data/mode_c_output2.pdf
Binary file test-data/mode_c_output2.pdf has changed
diff -r d4db13c9dd7f -r abc464ca7260 test-data/mode_f_output2.pdf
Binary file test-data/mode_f_output2.pdf has changed
diff -r d4db13c9dd7f -r abc464ca7260 test-data/mode_p_output2.pdf
Binary file test-data/mode_p_output2.pdf has changed
diff -r d4db13c9dd7f -r abc464ca7260 tool_dependencies.xml
--- a/tool_dependencies.xml Wed Dec 23 09:26:01 2015 -0500
+++ b/tool_dependencies.xml Tue Jul 26 06:06:17 2016 -0400
@@ -1,6 +1,6 @@
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+