Mercurial > repos > iuc > genetrack

changeset 1:df7ac50ade5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit 6cd0f93f4eb8649802683ae4c189c8ad48827a49
author iuc
date Fri, 13 Jan 2017 10:20:48 -0500
parents 25cd59a002d9
children aaca27a5263b
files genetrack.xml genetrack_macros.xml genetrack_util.py genetrack_util.pyc tool_dependencies.xml
diffstat 5 files changed, 9 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/genetrack.xml	Tue Dec 22 17:03:27 2015 -0500
+++ b/genetrack.xml	Fri Jan 13 10:20:48 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.0">
+<tool id="genetrack" name="GeneTrack" version="@WRAPPER_VERSION@.1">
     <description>peak predictor</description>
     <macros>
         <import>genetrack_macros.xml</import>
--- a/genetrack_macros.xml	Tue Dec 22 17:03:27 2015 -0500
+++ b/genetrack_macros.xml	Fri Jan 13 10:20:48 2017 -0500
@@ -3,7 +3,7 @@
     <token name="@WRAPPER_VERSION@">1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.3.0">anaconda</requirement>
+            <requirement type="package" version="1.11.3">numpy</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
--- a/genetrack_util.py	Tue Dec 22 17:03:27 2015 -0500
+++ b/genetrack_util.py	Fri Jan 13 10:20:48 2017 -0500
@@ -257,7 +257,7 @@
     lo, hi = get_range(data)
     rng = hi - lo
     shift = width - lo
-    return numpy.zeros(rng+width*2, numpy.float), shift
+    return numpy.zeros(rng + width * 2, numpy.float), shift
 
 
 def normal_array(width, sigma, normalize=True):
@@ -274,7 +274,7 @@
     values = numpy.array(values, numpy.float)
     # normalization
     if normalize:
-        values = 1.0/math.sqrt(2 * numpy.pi * sigma2) * values
+        values = 1.0 / math.sqrt(2 * numpy.pi * sigma2) * values
     return values
 
 
@@ -292,7 +292,7 @@
             if direction == 2:
                 # Swap positive and negative widths
                 pos, neg = neg, pos
-            peaks.append(Peak(int(index)-shift, pos, neg))
+            peaks.append(Peak(int(index) - shift, pos, neg))
     find_peaks()
 
     def calculate_reads():
@@ -313,8 +313,8 @@
         for peak in peaks_by_value:
             peak.safe = True
             window = get_window(peaks,
-                                peak.index-exclusion//2,
-                                peak.index+exclusion//2,
+                                peak.index - exclusion // 2,
+                                peak.index + exclusion // 2,
                                 peak_keys)
             for excluded in window:
                 if excluded.safe:
@@ -346,9 +346,9 @@
             index, forward, reverse = read
             # Add the normals to the appropriate regions
             if forward:
-                forward_array[index+forward_shift-width:index+forward_shift+width] += normal * forward
+                forward_array[index + forward_shift - width:index + forward_shift + width] += normal * forward
             if reverse:
-                reverse_array[index+reverse_shift-width:index+reverse_shift+width] += normal * reverse
+                reverse_array[index + reverse_shift - width:index + reverse_shift + width] += normal * reverse
     populate_array()
     forward_peaks = call_peaks(forward_array, forward_shift, data, keys, 1, down_width, up_width, exclusion)
     reverse_peaks = call_peaks(reverse_array, reverse_shift, data, keys, 2, down_width, up_width, exclusion)
Binary file genetrack_util.pyc has changed
--- a/tool_dependencies.xml	Tue Dec 22 17:03:27 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="anaconda" version="2.3.0">
-        <repository changeset_revision="94d978ebbfd4" name="package_anaconda_2_3_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>