diff --git a/tool_conf.xml.main b/tool_conf.xml.main index 3ad306b1422..b1b0ccb5dd5 100644 --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -284,8 +284,6 @@
- -
diff --git a/tools/genetrack/genetrack_indexer.py b/tools/genetrack/genetrack_indexer.py deleted file mode 100644 index 99d50d3ee0f..00000000000 --- 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 --git a/tools/genetrack/genetrack_indexer.xml b/tools/genetrack/genetrack_indexer.xml deleted file mode 100644 index fbd22d472e5..00000000000 --- a/tools/genetrack/genetrack_indexer.xml +++ /dev/null @@ -1,64 +0,0 @@ - - - on a BED file - - - genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x - - - - - - - - - - - - - - - - - - - - - -**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.* - - - - diff --git a/tools/genetrack/genetrack_peak_prediction.py b/tools/genetrack/genetrack_peak_prediction.py deleted file mode 100644 index 6b4598a9234..00000000000 --- 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 --git a/tools/genetrack/genetrack_peak_prediction.xml b/tools/genetrack/genetrack_peak_prediction.xml deleted file mode 100644 index 92a86582434..00000000000 --- a/tools/genetrack/genetrack_peak_prediction.xml +++ /dev/null @@ -1,69 +0,0 @@ - - - on GeneTrack index - - - genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 -x - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**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.* - - - -