2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63006e23bf7d/ Changeset: 63006e23bf7d Branch: stable User: natefoo Date: 2013-11-30 18:46:53 Summary: Remove broken GeneTrack tools. Affected #: 6 files diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -284,8 +284,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -345,8 +345,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - - <!-- this parameter is currently not used, may not be feasible to use it - <param name="coverage" type="select" label="Full coverage"> - <option value="no">NO</option> - <option value="yes">YES</option> - </param> - --> - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -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>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r 3b6cdcd9759595335cacd06b960efa6d96faaf72 -r 63006e23bf7d32e18033e0e59c0c194259935f6d tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> - <!-- <option value="yes">Moving averages</option> --> - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> - <!-- <option value="above">Above a threshold</option> --> - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> - <!-- <option value="yes1">Above a threshold</option> --> - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -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>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> https://bitbucket.org/galaxy/galaxy-central/commits/a508799de645/ Changeset: a508799de645 User: natefoo Date: 2013-11-30 18:47:19 Summary: merge stable. Affected #: 6 files diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -280,8 +280,6 @@ <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-rna-tools" name="NGS: RNA Analysis"><label id="rna_seq" text="RNA-seq" /> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -340,8 +340,6 @@ <tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /> - <tool file="genetrack/genetrack_indexer.xml" /> - <tool file="genetrack/genetrack_peak_prediction.xml" /></section><section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_indexer.py --- a/tools/genetrack/genetrack_indexer.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. - -usage: %prog input output shift -""" - -import sys, shutil, os -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import tabs2genetrack -from genetrack import logger - -if __name__ == "__main__": - import os - os.environ[ 'LC_ALL' ] = 'C' - #os.system( 'export' ) - - parser = tabs2genetrack.option_parser() - - options, args = parser.parse_args() - - # uppercase the format - options.format = options.format.upper() - - if options.format not in ('BED', 'GFF'): - sys.stdout = sys.stderr - parser.print_help() - sys.exit(-1) - - logger.disable(options.verbosity) - - # missing file names - if not (options.inpname and options.outname and options.format): - parser.print_help() - sys.exit(-1) - else: - tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ - format=options.format, shift=options.shift, index=options.index, options=options) diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ -<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> - - <description>on a BED file</description> - - <command interpreter="python"> - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - </command> - - <inputs> - - <param format="bed6" name="input" type="data" help="Input data"> - <label>Select input bed file</label> - </param> - - <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> - <label>Shift at 5' end</label> - </param> - - <!-- this parameter is currently not used, may not be feasible to use it - <param name="coverage" type="select" label="Full coverage"> - <option value="no">NO</option> - <option value="yes">YES</option> - </param> - --> - - </inputs> - - <outputs> - <data format="genetrack" name="output" /> - </outputs> - -<help> -**Help** - -This tool will create a visualization of the bed file that is selected. - -**Parameters** - -- **Shift at 5' end** should be used when the location of interest is at a fixed distance from - the 5' end for **all sequenced fragments**! - - For example if the sequenced sample consists - mono-nucleosomal DNA (146bp) we should expect that - each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. - Therefore we would enter 73 as the shift parameter. Once corrected the reads - on each strand will coincide and indicate the actual midpoints - of the nucleosomes. - - When shifting the averaging process in GeneTrack is able correct for longer or shorter - than expected fragment sizes as long as the errors are reasonably random. - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -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>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_peak_prediction.py --- a/tools/genetrack/genetrack_peak_prediction.py +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env python - -""" -Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. - -usage: %prog input output level sigma mode exclusion strand -""" - -import sys -from galaxy import eggs -import pkg_resources -pkg_resources.require( "GeneTrack" ) - -from genetrack.scripts import peakpred -from genetrack import logger - -if __name__ == "__main__": - - parser = peakpred.option_parser() - - options, args = parser.parse_args() - - logger.disable(options.verbosity) - - from genetrack import conf - - # trigger test mode - if options.test: - options.inpname = conf.testdata('test-hdflib-input.gtrack') - options.outname = conf.testdata('predictions.bed') - - # missing input file name - if not options.inpname and not options.outname: - parser.print_help() - else: - print 'Sigma = %s' % options.sigma - print 'Minimum peak = %s' % options.level - print 'Peak-to-peak = %s' % options.exclude - - peakpred.predict(options.inpname, options.outname, options) diff -r 2b5329b6fba3a5d332e734139b30a14d48a680a3 -r a508799de64595113ad4d26b8f2f9df7b64f1f69 tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ -<tool id="predict2genetrack" name="Peak predictor"> - - <description>on GeneTrack index</description> - - <command interpreter="python"> - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - </command> - - <inputs> - - <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> - - <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> - <option value="gauss">Gaussian kernel</option> - <!-- <option value="yes">Moving averages</option> --> - </param> - - <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> - - - <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> - <option value="nolap">Maximal non-overlapping</option> - <!-- <option value="above">Above a threshold</option> --> - <option value="all">All peaks</option> - </param> - - <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> - </param> - - <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> - - <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> - <option value="all">Merge strands</option> - <!-- <option value="yes1">Above a threshold</option> --> - <option value="two">Separate strands</option> - </param> - - </inputs> - - <outputs> - <data format="bed" name="output" /> - </outputs> - -<help> -**Help** - -This tool will generate genome wide peak prediction from an index file. - -**Parameters** - -- **Smoothing method** the function used to average nearby values - -- **Smoothing value** the factor used in the method - -- **Prediction method** the function used to average nearby values - -See http://genetrack.bx.psu.edu/ for more information on GeneTrack. - ------- - -**Citation** - -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>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - -</help> - -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.