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