Mercurial > repos > devteam > kernel_canonical_correlation_analysis
changeset 0:7a092113eb8c draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 19 May 2014 12:34:54 -0400 |
| parents | |
| children | 5ce5a2adb875 |
| files | kcca.py kcca.xml test-data/1.tabular test-data/2.tabular test-data/cca_out1.tabular test-data/iris.tabular test-data/kcca_out1.tabular test-data/kcca_out2.tabular tool_dependencies.xml |
| diffstat | 9 files changed, 1116 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kcca.py Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,147 @@ +#!/usr/bin/env python + +""" +Run kernel CCA using kcca() from R 'kernlab' package + +usage: %prog [options] + -i, --input=i: Input file + -o, --output1=o: Summary output + -x, --x_cols=x: X-Variable columns + -y, --y_cols=y: Y-Variable columns + -k, --kernel=k: Kernel function + -f, --features=f: Number of canonical components to return + -s, --sigma=s: sigma + -d, --degree=d: degree + -l, --scale=l: scale + -t, --offset=t: offset + -r, --order=r: order + +usage: %prog input output1 x_cols y_cols kernel features sigma(or_None) degree(or_None) scale(or_None) offset(or_None) order(or_None) +""" + +import sys, string +from rpy import * +import numpy +from bx.cookbook import doc_optparse +import logging +log = logging.getLogger('kcca') + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +#Parse Command Line +options, args = doc_optparse.parse( __doc__ ) +#{'options= kernel': 'rbfdot', 'var_cols': '1,2,3,4', 'degree': 'None', 'output2': '/afs/bx.psu.edu/home/gua110/workspace/galaxy_bitbucket/database/files/000/dataset_260.dat', 'output1': '/afs/bx.psu.edu/home/gua110/workspace/galaxy_bitbucket/database/files/000/dataset_259.dat', 'scale': 'None', 'offset': 'None', 'input': '/afs/bx.psu.edu/home/gua110/workspace/galaxy_bitbucket/database/files/000/dataset_256.dat', 'sigma': '1.0', 'order': 'None'} + +infile = options.input +x_cols = options.x_cols.split(',') +y_cols = options.y_cols.split(',') +kernel = options.kernel +outfile = options.output1 +ncomps = int(options.features) +fout = open(outfile,'w') + +if ncomps < 1: + print "You chose to return '0' canonical components. Please try rerunning the tool with number of components = 1 or more." + sys.exit() +elems = [] +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +x_vals = [] +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) +y_vals = [] +for k,col in enumerate(y_cols): + y_cols[k] = int(col)-1 + y_vals.append([]) +NA = 'NA' +skipped = 0 +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.strip().split("\t") + valid_line = True + for col in x_cols+y_cols: + try: + assert float(fields[col]) + except: + skipped += 1 + valid_line = False + break + if valid_line: + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except: + xval = NaN + x_vals[k].append(xval) + for k,col in enumerate(y_cols): + try: + yval = float(fields[col]) + except: + yval = NaN + y_vals[k].append(yval) + except: + skipped += 1 + +x_vals1 = numpy.asarray(x_vals).transpose() +y_vals1 = numpy.asarray(y_vals).transpose() + +x_dat= r.list(array(x_vals1)) +y_dat= r.list(array(y_vals1)) + +try: + r.suppressWarnings(r.library('kernlab')) +except: + stop_err('Missing R library kernlab') + +set_default_mode(NO_CONVERSION) +if kernel=="rbfdot" or kernel=="anovadot": + pars = r.list(sigma=float(options.sigma)) +elif kernel=="polydot": + pars = r.list(degree=float(options.degree),scale=float(options.scale),offset=float(options.offset)) +elif kernel=="tanhdot": + pars = r.list(scale=float(options.scale),offset=float(options.offset)) +elif kernel=="besseldot": + pars = r.list(degree=float(options.degree),sigma=float(options.sigma),order=float(options.order)) +elif kernel=="anovadot": + pars = r.list(degree=float(options.degree),sigma=float(options.sigma)) +else: + pars = rlist() + +try: + kcc = r.kcca(x=x_dat, y=y_dat, kernel=kernel, kpar=pars, ncomps=ncomps) +except RException, rex: + raise + log.exception( rex ) + stop_err("Encountered error while performing kCCA on the input data: %s" %(rex)) + +set_default_mode(BASIC_CONVERSION) +kcor = r.kcor(kcc) +if ncomps == 1: + kcor = [kcor] +xcoef = r.xcoef(kcc) +ycoef = r.ycoef(kcc) + +print >>fout, "#Component\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)])) + +print >>fout, "#Correlation\t%s" %("\t".join(["%.4g" % el for el in kcor])) + +print >>fout, "#Estimated X-coefficients\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)])) +for obs,val in enumerate(xcoef): + print >>fout, "%s\t%s" %(obs+1, "\t".join(["%.4g" % el for el in val])) + +print >>fout, "#Estimated Y-coefficients\t%s" %("\t".join(["%s" % el for el in range(1,ncomps+1)])) +for obs,val in enumerate(ycoef): + print >>fout, "%s\t%s" %(obs+1, "\t".join(["%.4g" % el for el in val]))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kcca.xml Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,154 @@ +<tool id="kcca1" name="Kernel Canonical Correlation Analysis" version="1.0.0"> + <description> </description> + <requirements> + <requirement type="package" version="1.0.3">rpy</requirement> + <requirement type="package" version="2.11.0">R</requirement> + <requirement type="package" version="0.1-4">kernlab</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="0.7.1">bx-python</requirement> + </requirements> + <command interpreter="python"> + kcca.py + --input=$input1 + --output1=$out_file1 + --x_cols=$x_cols + --y_cols=$y_cols + --kernel=$kernelChoice.kernel + --features=$features + #if $kernelChoice.kernel == "rbfdot" or $kernelChoice.kernel == "anovadot": + --sigma=$kernelChoice.sigma + --degree="None" + --scale="None" + --offset="None" + --order="None" + #elif $kernelChoice.kernel == "polydot": + --sigma="None" + --degree=$kernelChoice.degree + --scale=$kernelChoice.scale + --offset=$kernelChoice.offset + --order="None" + #elif $kernelChoice.kernel == "tanhdot": + --sigma="None" + --degree="None" + --scale=$kernelChoice.scale + --offset=$kernelChoice.offset + --order="None" + #elif $kernelChoice.kernel == "besseldot": + --sigma=$kernelChoice.sigma + --degree=$kernelChoice.degree + --scale="None" + --offset="None" + --order=$kernelChoice.order + #elif $kernelChoice.kernel == "anovadot": + --sigma=$kernelChoice.sigma + --degree=$kernelChoice.degree + --scale="None" + --offset="None" + --order="None" + #else: + --sigma="None" + --degree="None" + --scale="None" + --offset="None" + --order="None" + #end if + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> + <param name="x_cols" label="Select columns containing X variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > + <validator type="no_options" message="Please select at least one column."/> + </param> + <param name="y_cols" label="Select columns containing Y variables " type="data_column" data_ref="input1" numerical="True" multiple="true" > + <validator type="no_options" message="Please select at least one column."/> + </param> + <param name="features" size="10" type="integer" value="2" label="Number of canonical components to return" help="Enter an integer value greater than 0"/> + <conditional name="kernelChoice"> + <param name="kernel" type="select" label="Kernel function"> + <option value="rbfdot" selected="true">Gaussian Radial Basis Function</option> + <option value="polydot">Polynomial</option> + <option value="vanilladot">Linear</option> + <option value="tanhdot">Hyperbolic</option> + <option value="laplacedot">Laplacian</option> + <option value="besseldot">Bessel</option> + <option value="anovadot">ANOVA Radial Basis Function</option> + <option value="splinedot">Spline</option> + </param> + <when value="vanilladot" /> + <when value="splinedot" /> + <when value="rbfdot"> + <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> + </when> + <when value="laplacedot"> + <param name="sigma" size="10" type="float" value="1" label="sigma (inverse kernel width)" /> + </when> + <when value="polydot"> + <param name="degree" size="10" type="float" value="1" label="degree" /> + <param name="scale" size="10" type="float" value="1" label="scale" /> + <param name="offset" size="10" type="float" value="1" label="offset" /> + </when> + <when value="tanhdot"> + <param name="scale" size="10" type="float" value="1" label="scale" /> + <param name="offset" size="10" type="float" value="1" label="offset" /> + </when> + <when value="besseldot"> + <param name="sigma" size="10" type="float" value="1" label="sigma" /> + <param name="order" size="10" type="float" value="1" label="order" /> + <param name="degree" size="10" type="float" value="1" label="degree" /> + </when> + <when value="anovadot"> + <param name="sigma" size="10" type="float" value="1" label="sigma" /> + <param name="degree" size="10" type="float" value="1" label="degree" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + </outputs> + <tests> + <test> + <param name="input1" value="iris.tabular"/> + <param name="x_cols" value="1,2"/> + <param name="y_cols" value="3,4"/> + <param name="kernel" value="anovadot"/> + <param name="features" value="4"/> + <param name="sigma" value="0.1"/> + <param name="degree" value="2"/> + <output name="out_file1" file="kcca_out1.tabular" compare="re_match"/> + </test> + <test> + <param name="input1" value="iris.tabular"/> + <param name="x_cols" value="3,4"/> + <param name="y_cols" value="1,2"/> + <param name="kernel" value="rbfdot"/> + <param name="features" value="2"/> + <param name="sigma" value="0.5"/> + <output name="out_file1" file="kcca_out2.tabular" compare="re_match"/> + </test> + </tests> + <help> + + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool uses functions from 'kernlab' library from R statistical package to perform Kernel Canonical Correlation Analysis (kCCA) on the input data. + +*Alexandros Karatzoglou, Alex Smola, Kurt Hornik, Achim Zeileis (2004). kernlab - An S4 Package for Kernel Methods in R. Journal of Statistical Software 11(9), 1-20. URL http://www.jstatsoft.org/v11/i09/* + +----- + +.. class:: warningmark + +**Note** + +This tool currently treats all variables as continuous numeric variables. Running the tool on categorical variables might result in incorrect results. Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.tabular Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,6 @@ +chr22 1000 NM_17 +chr22 2000 NM_18 +chr10 2200 NM_10 +chr10 hap test +chr10 1200 NM_11 +chr22 1600 NM_19 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.tabular Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,10 @@ +1 68 4.1 +2 71 4.6 +3 62 3.8 +4 75 4.4 +5 58 3.2 +6 60 3.1 +7 67 3.8 +8 68 4.1 +9 71 4.3 +10 69 3.7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cca_out1.tabular Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,22 @@ +#Component 1 2 +#Correlation 0.9409 0.1311 +#F-statistic 144.4 2.57 +#p-value 6.213e-68 0.1111 +#X-Coefficients 1 2 +c3 1.507 -3.378 +c4 -0.5372 3.659 +#Y-Coefficients 1 2 +c1 6.35 3.379 +c2 -2.66 6.67 +#X-Loadings 1 2 +c3 0.9894 0.1452 +c4 0.9133 0.4073 +#Y-Loadings 1 2 +c1 0.9289 0.3704 +c2 -0.4698 0.8828 +#X-CrossLoadings 1 2 +c3 0.9309 0.01904 +c4 0.8593 0.05339 +#Y-CrossLoadings 1 2 +c1 0.874 0.04855 +c2 -0.442 0.1157
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/iris.tabular Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,151 @@ +5.1 3.5 1.4 0.2 Iris-setosa +4.9 3.0 1.4 0.2 Iris-setosa +4.7 3.2 1.3 0.2 Iris-setosa +4.6 3.1 1.5 0.2 Iris-setosa +5.0 3.6 1.4 0.2 Iris-setosa +5.4 3.9 1.7 0.4 Iris-setosa +4.6 3.4 1.4 0.3 Iris-setosa +5.0 3.4 1.5 0.2 Iris-setosa +4.4 2.9 1.4 0.2 Iris-setosa +4.9 3.1 1.5 0.1 Iris-setosa +5.4 3.7 1.5 0.2 Iris-setosa +4.8 3.4 1.6 0.2 Iris-setosa +4.8 3.0 1.4 0.1 Iris-setosa +4.3 3.0 1.1 0.1 Iris-setosa +5.8 4.0 1.2 0.2 Iris-setosa +5.7 4.4 1.5 0.4 Iris-setosa +5.4 3.9 1.3 0.4 Iris-setosa +5.1 3.5 1.4 0.3 Iris-setosa +5.7 3.8 1.7 0.3 Iris-setosa +5.1 3.8 1.5 0.3 Iris-setosa +5.4 3.4 1.7 0.2 Iris-setosa +5.1 3.7 1.5 0.4 Iris-setosa +4.6 3.6 1.0 0.2 Iris-setosa +5.1 3.3 1.7 0.5 Iris-setosa +4.8 3.4 1.9 0.2 Iris-setosa +5.0 3.0 1.6 0.2 Iris-setosa +5.0 3.4 1.6 0.4 Iris-setosa +5.2 3.5 1.5 0.2 Iris-setosa +5.2 3.4 1.4 0.2 Iris-setosa +4.7 3.2 1.6 0.2 Iris-setosa +4.8 3.1 1.6 0.2 Iris-setosa +5.4 3.4 1.5 0.4 Iris-setosa +5.2 4.1 1.5 0.1 Iris-setosa +5.5 4.2 1.4 0.2 Iris-setosa +4.9 3.1 1.5 0.1 Iris-setosa +5.0 3.2 1.2 0.2 Iris-setosa +5.5 3.5 1.3 0.2 Iris-setosa +4.9 3.1 1.5 0.1 Iris-setosa +4.4 3.0 1.3 0.2 Iris-setosa +5.1 3.4 1.5 0.2 Iris-setosa +5.0 3.5 1.3 0.3 Iris-setosa +4.5 2.3 1.3 0.3 Iris-setosa +4.4 3.2 1.3 0.2 Iris-setosa +5.0 3.5 1.6 0.6 Iris-setosa +5.1 3.8 1.9 0.4 Iris-setosa +4.8 3.0 1.4 0.3 Iris-setosa +5.1 3.8 1.6 0.2 Iris-setosa +4.6 3.2 1.4 0.2 Iris-setosa +5.3 3.7 1.5 0.2 Iris-setosa +5.0 3.3 1.4 0.2 Iris-setosa +7.0 3.2 4.7 1.4 Iris-versicolor +6.4 3.2 4.5 1.5 Iris-versicolor +6.9 3.1 4.9 1.5 Iris-versicolor +5.5 2.3 4.0 1.3 Iris-versicolor +6.5 2.8 4.6 1.5 Iris-versicolor +5.7 2.8 4.5 1.3 Iris-versicolor +6.3 3.3 4.7 1.6 Iris-versicolor +4.9 2.4 3.3 1.0 Iris-versicolor +6.6 2.9 4.6 1.3 Iris-versicolor +5.2 2.7 3.9 1.4 Iris-versicolor +5.0 2.0 3.5 1.0 Iris-versicolor +5.9 3.0 4.2 1.5 Iris-versicolor +6.0 2.2 4.0 1.0 Iris-versicolor +6.1 2.9 4.7 1.4 Iris-versicolor +5.6 2.9 3.6 1.3 Iris-versicolor +6.7 3.1 4.4 1.4 Iris-versicolor +5.6 3.0 4.5 1.5 Iris-versicolor +5.8 2.7 4.1 1.0 Iris-versicolor +6.2 2.2 4.5 1.5 Iris-versicolor +5.6 2.5 3.9 1.1 Iris-versicolor +5.9 3.2 4.8 1.8 Iris-versicolor +6.1 2.8 4.0 1.3 Iris-versicolor +6.3 2.5 4.9 1.5 Iris-versicolor +6.1 2.8 4.7 1.2 Iris-versicolor +6.4 2.9 4.3 1.3 Iris-versicolor +6.6 3.0 4.4 1.4 Iris-versicolor +6.8 2.8 4.8 1.4 Iris-versicolor +6.7 3.0 5.0 1.7 Iris-versicolor +6.0 2.9 4.5 1.5 Iris-versicolor +5.7 2.6 3.5 1.0 Iris-versicolor +5.5 2.4 3.8 1.1 Iris-versicolor +5.5 2.4 3.7 1.0 Iris-versicolor +5.8 2.7 3.9 1.2 Iris-versicolor +6.0 2.7 5.1 1.6 Iris-versicolor +5.4 3.0 4.5 1.5 Iris-versicolor +6.0 3.4 4.5 1.6 Iris-versicolor +6.7 3.1 4.7 1.5 Iris-versicolor +6.3 2.3 4.4 1.3 Iris-versicolor +5.6 3.0 4.1 1.3 Iris-versicolor +5.5 2.5 4.0 1.3 Iris-versicolor +5.5 2.6 4.4 1.2 Iris-versicolor +6.1 3.0 4.6 1.4 Iris-versicolor +5.8 2.6 4.0 1.2 Iris-versicolor +5.0 2.3 3.3 1.0 Iris-versicolor +5.6 2.7 4.2 1.3 Iris-versicolor +5.7 3.0 4.2 1.2 Iris-versicolor +5.7 2.9 4.2 1.3 Iris-versicolor +6.2 2.9 4.3 1.3 Iris-versicolor +5.1 2.5 3.0 1.1 Iris-versicolor +5.7 2.8 4.1 1.3 Iris-versicolor +6.3 3.3 6.0 2.5 Iris-virginica +5.8 2.7 5.1 1.9 Iris-virginica +7.1 3.0 5.9 2.1 Iris-virginica +6.3 2.9 5.6 1.8 Iris-virginica +6.5 3.0 5.8 2.2 Iris-virginica +7.6 3.0 6.6 2.1 Iris-virginica +4.9 2.5 4.5 1.7 Iris-virginica +7.3 2.9 6.3 1.8 Iris-virginica +6.7 2.5 5.8 1.8 Iris-virginica +7.2 3.6 6.1 2.5 Iris-virginica +6.5 3.2 5.1 2.0 Iris-virginica +6.4 2.7 5.3 1.9 Iris-virginica +6.8 3.0 5.5 2.1 Iris-virginica +5.7 2.5 5.0 2.0 Iris-virginica +5.8 2.8 5.1 2.4 Iris-virginica +6.4 3.2 5.3 2.3 Iris-virginica +6.5 3.0 5.5 1.8 Iris-virginica +7.7 3.8 6.7 2.2 Iris-virginica +7.7 2.6 6.9 2.3 Iris-virginica +6.0 2.2 5.0 1.5 Iris-virginica +6.9 3.2 5.7 2.3 Iris-virginica +5.6 2.8 4.9 2.0 Iris-virginica +7.7 2.8 6.7 2.0 Iris-virginica +6.3 2.7 4.9 1.8 Iris-virginica +6.7 3.3 5.7 2.1 Iris-virginica +7.2 3.2 6.0 1.8 Iris-virginica +6.2 2.8 4.8 1.8 Iris-virginica +6.1 3.0 4.9 1.8 Iris-virginica +6.4 2.8 5.6 2.1 Iris-virginica +7.2 3.0 5.8 1.6 Iris-virginica +7.4 2.8 6.1 1.9 Iris-virginica +7.9 3.8 6.4 2.0 Iris-virginica +6.4 2.8 5.6 2.2 Iris-virginica +6.3 2.8 5.1 1.5 Iris-virginica +6.1 2.6 5.6 1.4 Iris-virginica +7.7 3.0 6.1 2.3 Iris-virginica +6.3 3.4 5.6 2.4 Iris-virginica +6.4 3.1 5.5 1.8 Iris-virginica +6.0 3.0 4.8 1.8 Iris-virginica +6.9 3.1 5.4 2.1 Iris-virginica +6.7 3.1 5.6 2.4 Iris-virginica +6.9 3.1 5.1 2.3 Iris-virginica +5.8 2.7 5.1 1.9 Iris-virginica +6.8 3.2 5.9 2.3 Iris-virginica +6.7 3.3 5.7 2.5 Iris-virginica +6.7 3.0 5.2 2.3 Iris-virginica +6.3 2.5 5.0 1.9 Iris-virginica +6.5 3.0 5.2 2.0 Iris-virginica +6.2 3.4 5.4 2.3 Iris-virginica +5.9 3.0 5.1 1.8 Iris-virginica +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kcca_out1.tabular Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,304 @@ +\#Component\ 1\ 2\ 3\ 4 +\#Correlation\ \-?0\.99\d*\ \-?0\.99\d*\ \-?0\.93\d*\ \-?0\.93\d* +\#Estimated\ X\-?coefficients\ 1\ 2\ 3\ 4 +1\ \-?0\.0015\d*\ \-?0\.0015\d*\ \-?0\.034\d*\ \-?0\.034\d* +2\ \-?0\.001\d*\ \-?0\.001\d*\ \-?0\.032\d*\ \-?0\.032\d* +3\ \-?0\.0001\d*\ \-?0\.0001\d*\ \-?0\.018\d*\ \-?0\.018\d* +4\ \-?0\.0010\d*\ \-?0\.0010\d*\ \-?0\.0048\d*\ \-?0\.0048\d* +5\ \-?0\.000\d*\ \-?0\.000\d*\ \-?0\.052\d*\ \-?0\.052\d* +6\ \-?0\.0023\d*\ \-?0\.0023\d*\ \-?0\.019\d*\ \-?0\.019\d* +7\ \-?0\.0014\d*\ \-?0\.0014\d*\ \-?0\.0057\d*\ \-?0\.0057\d* +8\ \-?0\.0015\d*\ \-?0\.0015\d*\ \-?0\.038\d*\ \-?0\.038\d* +9\ \-?0\.0036\d*\ \-?0\.0036\d*\ \-?0\.07\d*\ \-?0\.07\d* +\d*\ \-?0\.0013\d*\ \-?0\.0013\d*\ \-?0\.031\d*\ \-?0\.031\d* +\d*\ \-?0\.0008\d*\ \-?0\.0008\d*\ \-?0\.0013\d*\ \-?0\.0013\d* +\d*\ \-?0\.00\d*\ \-?0\.00\d*\ \-?0\.039\d*\ \-?0\.039\d* 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 19 12:34:54 2014 -0400 @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="rpy" version="1.0.3"> + <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bx-python" version="0.7.1"> + <repository changeset_revision="2d0c08728bca" name="package_bx_python_0_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="2.11.0"> + <repository changeset_revision="5824d2b3bc8b" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="kernlab" version="0.1-4"> + <repository changeset_revision="ea1da94c31c2" name="package_cran_kernlab_0_1_4" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>