1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c7e8a024e94/ Changeset: 3c7e8a024e94 User: inithello Date: 2014-02-14 18:34:58 Summary: Remove stats/wiggle_to_simple, which is an exact duplicate of filters/wiggle_to_simple. Affected #: 4 files diff -r 128cbb948cc49ef2a08953f3facd59c409344e56 -r 3c7e8a024e9436eb2d7e970b7721f691728c4dae tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -95,7 +95,7 @@ <tool file="maf/maf_reverse_complement.xml" /></section><section id="scores" name="Get Genomic Scores"> - <tool file="stats/wiggle_to_simple.xml" /> + <tool file="filters/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /></section><section id="bxops" name="Operate on Genomic Intervals"> diff -r 128cbb948cc49ef2a08953f3facd59c409344e56 -r 3c7e8a024e9436eb2d7e970b7721f691728c4dae tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -104,7 +104,7 @@ <tool file="maf/maf_filter.xml" /></section><section id="scores" name="Get Genomic Scores"> - <tool file="stats/wiggle_to_simple.xml" /> + <tool file="filters/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /></section><section id="bxops" name="Operate on Genomic Intervals"> diff -r 128cbb948cc49ef2a08953f3facd59c409344e56 -r 3c7e8a024e9436eb2d7e970b7721f691728c4dae tools/stats/wiggle_to_simple.py --- a/tools/stats/wiggle_to_simple.py +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -""" -Read a wiggle track and print out a series of lines containing -"chrom position score". Ignores track lines, handles bed, variableStep -and fixedStep wiggle lines. -""" -import sys -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -import bx.wiggle -from galaxy.tools.exception_handling import * - -def stop_err( msg ): - sys.stderr.write( msg ) - sys.exit() - -def main(): - if len( sys.argv ) > 1: - in_file = open( sys.argv[1] ) - else: - in_file = open( sys.stdin ) - - if len( sys.argv ) > 2: - out_file = open( sys.argv[2], "w" ) - else: - out_file = sys.stdout - - try: - for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ): - out_file.write( "%s\n" % "\t".join( map( str, fields ) ) ) - except UCSCLimitException: - # Wiggle data was truncated, at the very least need to warn the user. - print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.' - except ValueError, e: - in_file.close() - out_file.close() - stop_err( str( e ) ) - - in_file.close() - out_file.close() - -if __name__ == "__main__": main() diff -r 128cbb948cc49ef2a08953f3facd59c409344e56 -r 3c7e8a024e9436eb2d7e970b7721f691728c4dae tools/stats/wiggle_to_simple.xml --- a/tools/stats/wiggle_to_simple.xml +++ /dev/null @@ -1,88 +0,0 @@ -<tool id="wiggle2simple1" name="Wiggle-to-Interval"> - <description>converter</description> - <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command> - <inputs> - <param format="wig" name="input" type="data" label="Convert"/> - </inputs> - <outputs> - <data format="interval" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input" value="2.wig" /> - <output name="out_file1" file="2.interval"/> - </test> - <test> - <param name="input" value="3.wig" /> - <output name="out_file1" file="3_wig.bed"/> - </test> - </tests> - <help> -**Syntax** - -This tool converts wiggle data into interval type. - -- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. - - - **BED format** with no declaration line and four columns of data:: - - chromA chromStartA chromEndA dataValueA - chromB chromStartB chromEndB dataValueB - - - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values:: - - variableStep chrom=chrN [span=windowSize] - chromStartA dataValueA - chromStartB dataValueB - - - **fixedStep** single column data; started by a declaration line and followed with data values:: - - fixedStep chrom=chrN start=position step=stepInterval [span=windowSize] - dataValue1 - dataValue2 - ------ - -**Example** - -- input wiggle format file:: - - #track type=wiggle_0 name="Bed Format" description="BED format" - chr19 59302000 59302300 -1.0 - chr19 59302300 59302600 -0.75 - chr19 59302600 59302900 -0.50 - chr19 59302900 59303200 -0.25 - chr19 59303200 59303500 0.0 - #track type=wiggle_0 name="variableStep" description="variableStep format" - variableStep chrom=chr19 span=150 - 59304701 10.0 - 59304901 12.5 - 59305401 15.0 - 59305601 17.5 - #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full - fixedStep chrom=chr19 start=59307401 step=300 span=200 - 1000 - 900 - 800 - 700 - 600 - -- convert the above file to interval file:: - - chr19 59302000 59302300 + -1.0 - chr19 59302300 59302600 + -0.75 - chr19 59302600 59302900 + -0.5 - chr19 59302900 59303200 + -0.25 - chr19 59303200 59303500 + 0.0 - chr19 59304701 59304851 + 10.0 - chr19 59304901 59305051 + 12.5 - chr19 59305401 59305551 + 15.0 - chr19 59305601 59305751 + 17.5 - chr19 59307701 59307901 + 1000.0 - chr19 59308001 59308201 + 900.0 - chr19 59308301 59308501 + 800.0 - chr19 59308601 59308801 + 700.0 - chr19 59308901 59309101 + 600.0 - -</help> -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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