| Previous changeset 0:25cd59a002d9 (2015-12-22) Next changeset 2:aaca27a5263b (2017-01-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit 6cd0f93f4eb8649802683ae4c189c8ad48827a49 |
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modified:
genetrack.xml genetrack_macros.xml genetrack_util.py |
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added:
genetrack_util.pyc |
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removed:
tool_dependencies.xml |
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| diff -r 25cd59a002d9 -r df7ac50ade5d genetrack.xml --- a/genetrack.xml Tue Dec 22 17:03:27 2015 -0500 +++ b/genetrack.xml Fri Jan 13 10:20:48 2017 -0500 |
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| @@ -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> |
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| diff -r 25cd59a002d9 -r df7ac50ade5d genetrack_macros.xml --- a/genetrack_macros.xml Tue Dec 22 17:03:27 2015 -0500 +++ b/genetrack_macros.xml Fri Jan 13 10:20:48 2017 -0500 |
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| @@ -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"> |
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| diff -r 25cd59a002d9 -r df7ac50ade5d genetrack_util.py --- a/genetrack_util.py Tue Dec 22 17:03:27 2015 -0500 +++ b/genetrack_util.py Fri Jan 13 10:20:48 2017 -0500 |
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| @@ -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) |
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| diff -r 25cd59a002d9 -r df7ac50ade5d genetrack_util.pyc |
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| Binary file genetrack_util.pyc has changed |
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| diff -r 25cd59a002d9 -r df7ac50ade5d tool_dependencies.xml --- a/tool_dependencies.xml Tue Dec 22 17:03:27 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |