| Previous changeset 0:369b8aa2f7bd (2013-01-17) Next changeset 2:e7295ec4e750 (2013-01-17) |
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Commit message:
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added:
idrPlotWrapper.sh |
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| diff -r 369b8aa2f7bd -r c6bfb8bcff93 idrPlotWrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idrPlotWrapper.sh Thu Jan 17 15:44:53 2013 -0500 |
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| @@ -0,0 +1,39 @@ +#!/bin/bash + +# idrPlotWrapper.sh +# OICR: Kar Ming Chu +# July 2012 + +# BASH wrapper for batch-consistency-plot.r (part of the IDR package) +# For use with Galaxy + +# Usage of batch-consistency-plot.r: Rscript batch-consistency-plot-merged.r [npairs] [output.dir] [input.file.prefix 1, 2, 3 ...] +# npairs - will be a constant, since Galaxy requires explicit control over input and output files + +# Usage of THIS SCRIPT: ./idrPlotWrapper.sh em uri outputfile +# em - em.sav file provided by Galaxy +# uri - uri.sav file provided by Galaxy +# outputfile - output file name specified by Galaxy + +main() { + EM="${1}" # absolute file path to em.sav file, provided by Galaxy + URI="${2}" # absolute file parth to uri.sav file, provided by Galaxy + OUTFILE="${3}" # name of desired output file + + cp "${EM}" ./idrPlot-em.sav # cp to this directory and rename so they can be found by idrPlot + cp "${URI}" ./idrPlot-uri.sav + + Rscript /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/idr/batch-consistency-plot.r 1 ./idrPlot idrPlot + + # convert post script to pdf file + ps2pdf ./idrPlot-plot.ps ./idrPlot-plot.pdf + + # rename to output file name + mv ./idrPlot-plot.pdf "${OUTFILE}" + + # clean up + rm idrPlot-em.sav + rm idrPlot-uri.sav +} + +main "${@}" |