Mercurial > repos > iuc > genetrack
changeset 4:b41a4bb828a3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack commit 2772547f531819d3f6d892ed041fa39b82e3550f
| author | iuc |
|---|---|
| date | Wed, 05 Jul 2017 11:56:54 -0400 |
| parents | 41887967ef14 |
| children | |
| files | genetrack.xml genetrack_macros.xml genetrack_util.py genetrack_util.pyc |
| diffstat | 4 files changed, 22 insertions(+), 28 deletions(-) [+] |
line wrap: on
line diff
--- a/genetrack.xml Sat Jan 21 14:41:43 2017 -0500 +++ b/genetrack.xml Wed Jul 05 11:56:54 2017 -0400 @@ -5,18 +5,18 @@ <import>genetrack_macros.xml</import> </macros> <expand macro="requirements" /> - <command> - python $__tool_directory__/genetrack.py - --input_format $input_format_cond.input_format - #for $i in $input_format_cond.input: - --input "${i}" "${i.hid}" - #end for - --sigma $sigma - --exclusion $exclusion - --up_width $up_width - --down_width $down_width - --filter $filter - </command> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/genetrack.py' +--input_format $input_format_cond.input_format +#for $i in $input_format_cond.input: + --input '${i}' '${i.hid}' +#end for +--sigma $sigma +--exclusion $exclusion +--up_width $up_width +--down_width $down_width +--filter $filter + ]]></command> <inputs> <conditional name="input_format_cond"> <param name="input_format" type="select" label="Format of files for conversion">
--- a/genetrack_macros.xml Sat Jan 21 14:41:43 2017 -0500 +++ b/genetrack_macros.xml Wed Jul 05 11:56:54 2017 -0400 @@ -3,17 +3,10 @@ <token name="@WRAPPER_VERSION@">1.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.11.3">numpy</requirement> + <requirement type="package" version="1.13.0">numpy</requirement> + <requirement type="package" version="1.10.0">six</requirement> </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1:"/> - <exit_code range=":-1"/> - <regex match="Error:"/> - <regex match="Exception:"/> - </stdio> - </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/btn119</citation>
--- a/genetrack_util.py Sat Jan 21 14:41:43 2017 -0500 +++ b/genetrack_util.py Wed Jul 05 11:56:54 2017 -0400 @@ -6,6 +6,7 @@ import tempfile import numpy +from six import Iterator GFF_EXT = 'gff' SCIDX_EXT = 'scidx' @@ -41,7 +42,7 @@ return data -class ChromosomeManager(object): +class ChromosomeManager(Iterator): """ Manages a CSV reader of an index file to only load one chrom at a time """ @@ -53,8 +54,8 @@ self.current_index = 0 self.next_valid() - def next(self): - self.line = self.reader.next() + def __next__(self): + self.line = next(self.reader) def is_valid(self, line): if len(line) not in [4, 5, 9]: @@ -77,10 +78,10 @@ """ Advance to the next valid line in the reader """ - self.line = self.reader.next() + self.line = next(self.reader) s = 0 while not self.is_valid(self.line): - self.line = self.reader.next() + self.line = next(self.reader) s += 1 if s > 0: # Skip initial line(s) of file @@ -115,7 +116,7 @@ self.current_index = read[0] self.add_read(read) try: - self.next() + next(self) except StopIteration: self.done = True break @@ -271,7 +272,7 @@ return math.exp(-x * x / (2 * sigma2)) # width is the half of the distribution - values = map(normal_func, range(-width, width)) + values = list(map(normal_func, range(-width, width))) values = numpy.array(values, numpy.float) # normalization if normalize: