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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Remove broken GeneTrack tools.
This commit is contained in:
Nate Coraor
@@ -284,8 +284,6 @@
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<section id="peak_calling" name="NGS: Peak Calling">
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<tool file="peak_calling/macs_wrapper.xml" />
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<tool file="peak_calling/sicer_wrapper.xml" />
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<tool file="genetrack/genetrack_indexer.xml" />
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<tool file="genetrack/genetrack_peak_prediction.xml" />
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</section>
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<section id="ngs-rna-tools" name="NGS: RNA Analysis">
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<label id="rna_seq" text="RNA-seq" />
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@@ -345,8 +345,6 @@
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<tool file="peak_calling/macs_wrapper.xml" />
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<tool file="peak_calling/sicer_wrapper.xml" />
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<tool file="peak_calling/ccat_wrapper.xml" />
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<tool file="genetrack/genetrack_indexer.xml" />
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<tool file="genetrack/genetrack_peak_prediction.xml" />
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</section>
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<section id="ngs-simulation" name="NGS: Simulation">
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<tool file="ngs_simulation/ngs_simulation.xml" />
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@@ -1,42 +0,0 @@
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#!/usr/bin/env python
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"""
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Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy.
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usage: %prog input output shift
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"""
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import sys, shutil, os
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "GeneTrack" )
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from genetrack.scripts import tabs2genetrack
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from genetrack import logger
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if __name__ == "__main__":
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import os
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os.environ[ 'LC_ALL' ] = 'C'
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#os.system( 'export' )
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parser = tabs2genetrack.option_parser()
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options, args = parser.parse_args()
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# uppercase the format
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options.format = options.format.upper()
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if options.format not in ('BED', 'GFF'):
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sys.stdout = sys.stderr
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parser.print_help()
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sys.exit(-1)
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logger.disable(options.verbosity)
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# missing file names
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if not (options.inpname and options.outname and options.format):
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parser.print_help()
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sys.exit(-1)
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else:
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tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
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format=options.format, shift=options.shift, index=options.index, options=options)
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@@ -1,64 +0,0 @@
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<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1">
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<description>on a BED file</description>
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<command interpreter="python">
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genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
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</command>
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<inputs>
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<param format="bed6" name="input" type="data" help="Input data">
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<label>Select input bed file</label>
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</param>
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<param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
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<label>Shift at 5' end</label>
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</param>
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<!-- this parameter is currently not used, may not be feasible to use it
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<param name="coverage" type="select" label="Full coverage">
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<option value="no">NO</option>
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<option value="yes">YES</option>
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</param>
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-->
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</inputs>
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<outputs>
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<data format="genetrack" name="output" />
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</outputs>
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<help>
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**Help**
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This tool will create a visualization of the bed file that is selected.
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**Parameters**
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- **Shift at 5' end** should be used when the location of interest is at a fixed distance from
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the 5' end for **all sequenced fragments**!
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For example if the sequenced sample consists
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mono-nucleosomal DNA (146bp) we should expect that
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each nucleosome midpoint is located at 73 bp from the 5' end of the fragment.
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Therefore we would enter 73 as the shift parameter. Once corrected the reads
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on each strand will coincide and indicate the actual midpoints
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of the nucleosomes.
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When shifting the averaging process in GeneTrack is able correct for longer or shorter
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than expected fragment sizes as long as the errors are reasonably random.
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See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
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------
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**Citation**
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For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_
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If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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</help>
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</tool>
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@@ -1,40 +0,0 @@
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#!/usr/bin/env python
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"""
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Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy.
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usage: %prog input output level sigma mode exclusion strand
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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
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pkg_resources.require( "GeneTrack" )
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from genetrack.scripts import peakpred
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from genetrack import logger
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if __name__ == "__main__":
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parser = peakpred.option_parser()
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options, args = parser.parse_args()
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logger.disable(options.verbosity)
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from genetrack import conf
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# trigger test mode
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if options.test:
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options.inpname = conf.testdata('test-hdflib-input.gtrack')
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options.outname = conf.testdata('predictions.bed')
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# missing input file name
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if not options.inpname and not options.outname:
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parser.print_help()
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else:
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print 'Sigma = %s' % options.sigma
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print 'Minimum peak = %s' % options.level
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print 'Peak-to-peak = %s' % options.exclude
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peakpred.predict(options.inpname, options.outname, options)
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@@ -1,69 +0,0 @@
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<tool id="predict2genetrack" name="Peak predictor">
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<description>on GeneTrack index</description>
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<command interpreter="python">
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genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x
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</command>
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<inputs>
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<param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/>
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<param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values">
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<option value="gauss">Gaussian kernel</option>
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<!-- <option value="yes">Moving averages</option> -->
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</param>
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<param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" />
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<param name="mode" type="select" label="Peak prediction" help="Peak prediction method">
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<option value="nolap">Maximal non-overlapping</option>
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<!-- <option value="above">Above a threshold</option> -->
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<option value="all">All peaks</option>
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</param>
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<param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance">
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</param>
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<param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" />
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<param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately">
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<option value="all">Merge strands</option>
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<!-- <option value="yes1">Above a threshold</option> -->
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<option value="two">Separate strands</option>
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</param>
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</inputs>
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<outputs>
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<data format="bed" name="output" />
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</outputs>
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<help>
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**Help**
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This tool will generate genome wide peak prediction from an index file.
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**Parameters**
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- **Smoothing method** the function used to average nearby values
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- **Smoothing value** the factor used in the method
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- **Prediction method** the function used to average nearby values
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See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
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------
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**Citation**
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For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_
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If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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</help>
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</tool>
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