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rgedgeR/rgToolFactory.py rgedgeR/rgedgeRpaired.xml rgedgeR/test-data/edgeRtest1out.html rgedgeR/test-data/edgeRtest1out.xls rgedgeR/test-data/gentestdata.sh rgedgeR/test-data/test_bams2mx.xls rgedgeR/tool_dependencies.xml |
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diff -r 643164729057 -r 91e77df18a7f rgedgeR/rgToolFactory.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/rgToolFactory.py Fri Jul 26 22:04:58 2013 -0400 |
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b'@@ -0,0 +1,599 @@\n+# rgToolFactory.py\n+# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home\n+# \n+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012\n+# \n+# all rights reserved\n+# Licensed under the LGPL\n+# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home\n+#\n+# july 2013\n+# added ability to combine images and individual log files into html output\n+# just make sure there\'s a log file foo.log and it will be output\n+# together with all images named like "foo_*.pdf\n+# otherwise old format for html\n+#\n+# January 2013\n+# problem pointed out by Carlos Borroto\n+# added escaping for <>$ - thought I did that ages ago...\n+#\n+# August 11 2012 \n+# changed to use shell=False and cl as a sequence\n+\n+# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.\n+# It also serves as the wrapper for the new tool.\n+# \n+# you paste and run your script\n+# Only works for simple scripts that read one input from the history.\n+# Optionally can write one new history dataset,\n+# and optionally collect any number of outputs into links on an autogenerated HTML page.\n+\n+# DO NOT install on a public or important site - please.\n+\n+# installed generated tools are fine if the script is safe.\n+# They just run normally and their user cannot do anything unusually insecure\n+# but please, practice safe toolshed.\n+# Read the fucking code before you install any tool \n+# especially this one\n+\n+# After you get the script working on some test data, you can\n+# optionally generate a toolshed compatible gzip file\n+# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for\n+# safe and largely automated installation in a production Galaxy.\n+\n+# If you opt for an HTML output, you get all the script outputs arranged\n+# as a single Html history item - all output files are linked, thumbnails for all the pdfs.\n+# Ugly but really inexpensive.\n+# \n+# Patches appreciated please. \n+#\n+#\n+# long route to June 2012 product\n+# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them\n+# derived from an integrated script model \n+# called rgBaseScriptWrapper.py\n+# Note to the unwary:\n+# This tool allows arbitrary scripting on your Galaxy as the Galaxy user\n+# There is nothing stopping a malicious user doing whatever they choose\n+# Extremely dangerous!!\n+# Totally insecure. So, trusted users only\n+#\n+# preferred model is a developer using their throw away workstation instance - ie a private site.\n+# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.\n+#\n+\n+import sys \n+import shutil \n+import subprocess \n+import os \n+import time \n+import tempfile \n+import optparse\n+import tarfile\n+import re\n+import shutil\n+import math\n+\n+progname = os.path.split(sys.argv[0])[1] \n+myversion = \'V000.2 June 2012\' \n+verbose = False \n+debug = False\n+toolFactoryURL = \'https://bitbucket.org/fubar/galaxytoolfactory\'\n+\n+def timenow():\n+ """return current time as a string\n+ """\n+ return time.strftime(\'%d/%m/%Y %H:%M:%S\', time.localtime(time.time()))\n+\n+html_escape_table = {\n+ "&": "&",\n+ ">": ">",\n+ "<": "<",\n+ "$": "\\$"\n+ }\n+\n+def html_escape(text):\n+ """Produce entities within text."""\n+ return "".join(html_escape_table.get(c,c) for c in text)\n+\n+def cmd_exists(cmd):\n+ return subprocess.call("type " + cmd, shell=True, \n+ stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0\n+\n+\n+class ScriptRunner:\n+ """class is a wrapper for an arbitrary script\n+ """\n+\n+ def __init__(self,opts=None,treatbashSpecial=True):\n+ """\n+ cleanup inputs, setup some outputs\n+ \n+ """\n+ self.useGM = cmd_exists(\'gm\')\n+ self.useIM = cmd_exists(\'convert\')\n+ self.useGS = cmd_exists(\'gs\')\n+ self.treatbashSpecial = treatbashSpecial\n+ if opts.output_dir: # simplify for the'..b'\\n\')\n+ fhtml.append(\'</table></div><br/>\')\n+ html.append(\'<div class="toolFormTitle">All output files available for downloading</div>\\n\')\n+ html += fhtml # add all non-pdf files to the end of the display\n+ else:\n+ html.append(\'<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>\' % self.opts.interpreter)\n+ html.append(galhtmlpostfix)\n+ htmlf = file(self.opts.output_html,\'w\')\n+ htmlf.write(\'\\n\'.join(html))\n+ htmlf.write(\'\\n\')\n+ htmlf.close()\n+ self.html = html\n+\n+\n+ def run(self):\n+ """\n+ scripts must be small enough not to fill the pipe!\n+ """\n+ if self.treatbashSpecial and self.opts.interpreter in [\'bash\',\'sh\']:\n+ retval = self.runBash()\n+ else:\n+ if self.opts.output_dir:\n+ sto = open(self.tlog,\'w\')\n+ sto.write(\'## Toolfactory generated command line = %s\\n\' % \' \'.join(self.cl))\n+ sto.flush()\n+ p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)\n+ else:\n+ p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)\n+ p.stdin.write(self.script)\n+ p.stdin.close()\n+ retval = p.wait()\n+ if self.opts.output_dir:\n+ sto.close()\n+ if self.opts.make_HTML:\n+ self.makeHtml()\n+ return retval\n+\n+ def runBash(self):\n+ """\n+ cannot use - for bash so use self.sfile\n+ """\n+ if self.opts.output_dir:\n+ s = \'## Toolfactory generated command line = %s\\n\' % \' \'.join(self.cl)\n+ sto = open(self.tlog,\'w\')\n+ sto.write(s)\n+ sto.flush()\n+ p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)\n+ else:\n+ p = subprocess.Popen(self.cl,shell=False) \n+ retval = p.wait()\n+ if self.opts.output_dir:\n+ sto.close()\n+ if self.opts.make_HTML:\n+ self.makeHtml()\n+ return retval\n+ \n+\n+def main():\n+ u = """\n+ This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:\n+ <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"\n+ </command>\n+ """\n+ op = optparse.OptionParser()\n+ a = op.add_option\n+ a(\'--script_path\',default=None)\n+ a(\'--tool_name\',default=None)\n+ a(\'--interpreter\',default=None)\n+ a(\'--output_dir\',default=None)\n+ a(\'--output_html\',default=None)\n+ a(\'--input_tab\',default="None")\n+ a(\'--output_tab\',default="None")\n+ a(\'--user_email\',default=\'Unknown\')\n+ a(\'--bad_user\',default=None)\n+ a(\'--make_Tool\',default=None)\n+ a(\'--make_HTML\',default=None)\n+ a(\'--help_text\',default=None)\n+ a(\'--tool_desc\',default=None)\n+ a(\'--new_tool\',default=None)\n+ a(\'--tool_version\',default=None)\n+ opts, args = op.parse_args()\n+ assert not opts.bad_user,\'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini\' % (opts.bad_user,opts.bad_user)\n+ assert opts.tool_name,\'## Tool Factory expects a tool name - eg --tool_name=DESeq\'\n+ assert opts.interpreter,\'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript\'\n+ assert os.path.isfile(opts.script_path),\'## Tool Factory wrapper expects a script path - eg --script_path=foo.R\'\n+ if opts.output_dir:\n+ try:\n+ os.makedirs(opts.output_dir)\n+ except:\n+ pass\n+ r = ScriptRunner(opts)\n+ if opts.make_Tool:\n+ retcode = r.makeTooltar()\n+ else:\n+ retcode = r.run()\n+ os.unlink(r.sfile)\n+ if retcode:\n+ sys.exit(retcode) # indicate failure to job runner\n+\n+\n+if __name__ == "__main__":\n+ main()\n+\n+\n' |
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diff -r 643164729057 -r 91e77df18a7f rgedgeR/rgedgeRpaired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/rgedgeRpaired.xml Fri Jul 26 22:04:58 2013 -0400 |
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b'@@ -0,0 +1,918 @@\n+<tool id="rgDifferentialCount" name="Differential_Count" version="0.20">\n+ <description>models using BioConductor packages</description>\n+ <requirements>\n+ <requirement type="package" version="2.12">biocbasics</requirement>\n+ <requirement type="package" version="3.0.1">package_r3</requirement>\n+ </requirements>\n+ \n+ <command interpreter="python">\n+ rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" \n+ --output_dir "$html_file.files_path" --output_html "$html_file" --output_tab "$outtab" --make_HTML "yes"\n+ </command>\n+ <inputs>\n+ <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"\n+ help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>\n+ <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" \n+ help="Supply a meaningful name here to remind you what the outputs contain">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits"><add value="_" /> </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>\n+ <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" \n+ multiple="true" use_header_names="true" size="120" display="checkboxes">\n+ <validator type="no_options" message="Please select at least one column."/>\n+ </param>\n+ <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>\n+ <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" \n+ multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">\n+ </param>\n+ <param name="subjectids" type="text" optional="true" size="120" value = ""\n+ label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in input"\n+ help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter \'1,2,1,2\'">\n+ <sanitizer>\n+ <valid initial="string.digits"><add value="," /> </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"\n+ help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>\n+ <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" \n+ label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"\n+ help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>\n+\n+ <conditional name="edgeR">\n+ <param name="doedgeR" type="select" \n+ label="Run this model using edgeR"\n+ help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">\n+ <option value="F">Do not run edgeR</option>\n+ <option value="T" selected="true">Run edgeR</option>\n+ </param>\n+ <when value="T">\n+ <param name="edgeR_priordf" type="integer" value="20" size="3" \n+ label="prior.df for tagwise dispersion - lower value = more emphasis on each tag\'s variance. Replaces prior.n and prior.df = prior.n * residual.df"\n+ help="0 = Use edgeR default. Use a small value to \'smooth\' small samples. See edgeR docs and note below"/>\n+ </when>\n+ <when value="F"> </when>\n+ </conditional>\n+ <conditional name="DESeq2">\n+ <param name="'..b'he excellent documentation and vignettes for the Bioconductor\n+packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.\n+\n+***old rant on changes to Bioconductor package variable names between versions***\n+\n+The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) \n+breaking this and all other code that assumed the old name for this variable, \n+between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). \n+This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing \n+to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly\n+when their old scripts break. This tool currently now works with 2.4.6.\n+\n+**Note on prior.N**\n+\n+http://seqanswers.com/forums/showthread.php?t=5591 says:\n+\n+*prior.n*\n+\n+The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. \n+You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood \n+in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your \n+tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the \n+common likelihood the weight of one observation.\n+\n+In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, \n+or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that \n+you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation \n+(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? \n+What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. \n+If you have more samples, then the tagwise dispersion estimates will be more reliable, \n+so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. \n+\n+\n+From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:\n+\n+Dear Dorota,\n+\n+The important settings are prior.df and trend.\n+\n+prior.n and prior.df are related through prior.df = prior.n * residual.df,\n+and your experiment has residual.df = 36 - 12 = 24. So the old setting of\n+prior.n=10 is equivalent for your data to prior.df = 240, a very large\n+value. Going the other way, the new setting of prior.df=10 is equivalent\n+to prior.n=10/24.\n+\n+To recover old results with the current software you would use\n+\n+ estimateTagwiseDisp(object, prior.df=240, trend="none")\n+\n+To get the new default from old software you would use\n+\n+ estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)\n+\n+Actually the old trend method is equivalent to trend="loess" in the new\n+software. You should use plotBCV(object) to see whether a trend is\n+required.\n+\n+Note you could also use\n+\n+ prior.n = getPriorN(object, prior.df=10)\n+\n+to map between prior.df and prior.n.\n+\n+----\n+\n+**Attributions**\n+\n+edgeR - edgeR_ \n+\n+VOOM/limma - limma_VOOM_ \n+\n+DESeq2 - DESeq2_ for details\n+\n+See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.\n+\n+Galaxy_ (that\'s what you are using right now!) for gluing everything together \n+\n+Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is \n+licensed to you under the LGPL_ like other rgenetics artefacts\n+\n+.. _LGPL: http://www.gnu.org/copyleft/lesser.html\n+.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html\n+.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html\n+.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html\n+.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html\n+.. _Galaxy: http://getgalaxy.org\n+</help>\n+\n+</tool>\n+\n+\n' |
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diff -r 643164729057 -r 91e77df18a7f rgedgeR/test-data/edgeRtest1out.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/test-data/edgeRtest1out.html Fri Jul 26 22:04:58 2013 -0400 |
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b'@@ -0,0 +1,813 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> \n+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> \n+ <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> \n+ <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> \n+ <title></title> \n+ <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> \n+ </head> \n+ <body> \n+ <div class="toolFormBody"> \n+ \n+<div class="infomessage">Galaxy Tool "edgeR" run at 12/06/2013 16:42:51</div><br/>\n+<div><table class="simple" cellpadding="2" cellspacing="2">\n+<tr>\n+<td><a href="edgeRtest_BCV_vs_abundance.pdf"><img src="edgeRtest_BCV_vs_abundance.jpg" title="Click to download a PDF of edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_BCV_vs_abundance.pdf"/></a></td>\n+\n+<td><a href="edgeRtest_MDSplot.pdf"><img src="edgeRtest_MDSplot.jpg" title="Click to download a PDF of edgeRtest_MDSplot.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_MDSplot.pdf"/></a></td>\n+\n+<td><a href="edgeRtest_RowsumCum.pdf"><img src="edgeRtest_RowsumCum.jpg" title="Click to download a PDF of edgeRtest_RowsumCum.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_RowsumCum.pdf"/></a></td>\n+</tr>\n+<tr>\n+<td><a href="edgeRtest_Smearplot.pdf"><img src="edgeRtest_Smearplot.jpg" title="Click to download a PDF of edgeRtest_Smearplot.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_Smearplot.pdf"/></a></td>\n+\n+<td><a href="edgeRtest_heatmap.pdf"><img src="edgeRtest_heatmap.jpg" title="Click to download a PDF of edgeRtest_heatmap.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_heatmap.pdf"/></a></td>\n+\n+<td><a href="edgeRtest_pval_qq.pdf"><img src="edgeRtest_pval_qq.jpg" title="Click to download a PDF of edgeRtest_pval_qq.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_pval_qq.pdf"/></a></td>\n+</tr>\n+<tr>\n+<td><a href="edgeRtest_sampleBoxplot.pdf"><img src="edgeRtest_sampleBoxplot.jpg" title="Click to download a PDF of edgeRtest_sampleBoxplot.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_sampleBoxplot.pdf"/></a></td>\n+\n+<td><a href="edgeRtest_samplehistplot.pdf"><img src="edgeRtest_samplehistplot.jpg" title="Click to download a PDF of edgeRtest_samplehistplot.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_samplehistplot.pdf"/></a></td>\n+\n+<td><a href="edgeRtest_venn.pdf"><img src="edgeRtest_venn.jpg" title="Click to download a PDF of edgeRtest_venn.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_venn.pdf"/></a></td>\n+</tr>\n+<tr>\n+<td><a href="edgeRtest_voomplot.pdf"><img src="edgeRtest_voomplot.jpg" title="Click to download a PDF of edgeRtest_voomplot.pdf" hspace="5" width="400" \n+ alt="Image called edgeRtest_voomplot.pdf"/></a></td>\n+\n+<td> </td><td> </td>\n+</tr></table></div>\n+\n+<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n+\n+<tr><td><a href="edgeR.Rscript">edgeR.Rscript</a></td><td>19.7 KB)</td></tr>\n+<tr class="odd_row"><td><a href="edgeR_runner.log">edgeR_runner.log</a></td><td>79.2 KB)</td></tr>\n+<tr><td><a href="edgeRtest_BCV_vs_abundance.pdf">edgeRtest_BCV_vs_abundance.pdf</a></td><td>16.4 KB)</td></tr>\n+<tr class="odd_row"><td><a href="edgeRtest_DESeq_TopTable.xls">edgeRtest_DESeq_TopTable.xls</a></td><td>135.1 KB)</td></tr>\n+<tr><td><a href="edgeRtest_MDSplot.pdf">edgeRtest_MDSplot.pdf</a></td><td>4.9 KB)</td></tr>\n+<tr class="odd_row"><td><a href="edgeRtest_RowsumCum.pdf">edgeRtest_RowsumCum.pdf</a></td><td>6.3 KB)</td></tr>\n+<tr><td><a hr'..b'+\n+655 Mir215 3.045873 5.7544234 11.148134 2.141822e-08 8.082459e-07 9.753268\n+\n+628 Mir1983 5.895500 0.9931851 11.445812 1.527548e-08 6.441605e-07 9.749260\n+\n+344 Dnm3os 3.363344 5.8607432 11.092261 2.283960e-08 8.082459e-07 9.689496\n+\n+637 Mir200a -6.191561 1.7981309 -11.322172 1.756229e-08 6.909853e-07 9.662295\n+\n+587 Mir182 -4.903995 7.1511683 -11.074468 2.331304e-08 8.082459e-07 9.658842\n+\n+582 Mir181a-2 3.048298 6.9414651 11.072128 2.337609e-08 8.082459e-07 9.644017\n+\n+614 Mir1948 -7.195525 4.5513493 -11.005492 2.524936e-08 8.473388e-07 9.341794\n+\n+654 Mir214 3.280874 5.4784451 10.768257 3.332555e-08 1.086413e-06 9.318504\n+\n+571 Mir153 5.963803 1.4386315 10.727082 3.498742e-08 1.093990e-06 9.035569\n+\n+318 Cyp3a25 -6.318200 1.4888933 -10.698226 3.620443e-08 1.093990e-06 9.024973\n+\n+464 Gm5441 5.982176 1.4484953 10.692891 3.643436e-08 1.093990e-06 9.000362\n+\n+541 Mir125b-2 3.077678 7.4316058 10.446668 4.893073e-08 1.431538e-06 8.884250\n+\n+551 Mir133a-1 5.144671 0.5903264 10.358205 5.447229e-08 1.553822e-06 8.575535\n+\n+550 Mir132 2.847559 5.3211839 10.110952 7.380297e-08 2.004981e-06 8.531491\n+\n+13 1110038B12Rik -2.226702 10.8487089 -10.194609 6.655312e-08 1.852125e-06 8.439308\n+\n+922 Rabggtb -1.935779 9.9874171 -9.928995 9.262821e-08 2.457879e-06 8.133384\n+\n+569 Mir150 2.938531 7.6297870 9.842102 1.033602e-07 2.620755e-06 8.116464\n+\n+800 Mir504 5.256127 0.6221088 9.892894 9.693595e-08 2.513725e-06 8.068853\n+\n+573 Mir155 3.906600 3.9899000 9.732173 1.188627e-07 2.712448e-06 8.046518\n+\n+666 Mir24-2 2.833979 7.3083691 9.767192 1.136724e-07 2.646944e-06 8.030550\n+\n+700 Mir3074-2 2.833979 7.3083691 9.767192 1.136724e-07 2.646944e-06 8.030550\n+\n+664 Mir23b 2.124129 9.8141190 9.806316 1.081569e-07 2.625681e-06 7.979464\n+\n+631 Mir199b 5.752816 2.8805143 9.823920 1.057683e-07 2.623514e-06 7.979387\n+\n+Warning messages:\n+\n+1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == :\n+\n+ Outlier (-Inf) in boxplot 5 is not drawn\n+\n+2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == :\n+\n+ Outlier (-Inf) in boxplot 7 is not drawn\n+\n+3: In bxp(list(stats = c(-Inf, -Inf, -0.158608221176912, 0.826586442285183, :\n+\n+ some notches went outside hinges (\'box\'): maybe set notch=FALSE\n+\n+4: In par(defpar) : calling par(new=TRUE) with no plot\n+\n+R version 2.15.1 (2012-06-22)\n+\n+Platform: x86_64-unknown-linux-gnu (64-bit)\n+\n+locale:\n+\n+ [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C \n+\n+attached base packages:\n+\n+[1] methods grid stats graphics grDevices utils datasets base \n+\n+other attached packages:\n+\n+ [1] edgeR_3.0.8 limma_3.14.4 DESeq_1.10.1 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.18.0 BiocGenerics_0.4.0 gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 gtools_2.7.1 stringr_0.6.2 \n+\n+loaded via a namespace (and not attached):\n+\n+ [1] annotate_1.36.0 AnnotationDbi_1.20.7 bitops_1.0-5 DBI_0.2-7 genefilter_1.40.0 geneplotter_1.36.0 IRanges_1.16.6 parallel_2.15.1 RColorBrewer_1.0-5 RSQLite_0.11.3 splines_2.15.1 stats4_2.15.1 survival_2.37-4 XML_3.96-1.1 xtable_1.7-1 \n+\n+</pre>\n+\n+<hr/><div class="infomessage">This tool (edgeR) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>\n+</div></body></html>\n+\n' |
b |
diff -r 643164729057 -r 91e77df18a7f rgedgeR/test-data/edgeRtest1out.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/test-data/edgeRtest1out.xls Fri Jul 26 22:04:58 2013 -0400 |
b |
b'@@ -0,0 +1,1142 @@\n+Name\tlogFC\tlogCPM\tLR\tPValue\tadj.p.value\tDispersion\ttotreads\tcase_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcase_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tcontrol_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam\n+Mir122a\t-10.6613482198735\t12.5379487184339\t445.912028851371\t5.59474310450852e-99\t6.38360188224422e-96\t0.102055096028295\t90428\t6.64466912039531\t2.86464823551992\t20.1236936368881\t4.75652253016081\t20841.6623198401\t16818.9531619257\t7242.55663282834\t8468.31297344994\t12\t7\t27\t8\t29767\t24233\t11911\t24463\n+Mir192\t-7.10901851688288\t17.2474145508888\t366.131659138235\t1.3015583263717e-81\t7.42539025195057e-79\t0.0776548700185199\t2325567\t1779.66387941254\t1294.41176699279\t4493.54625691845\t1933.52640851037\t463599.032378899\t340312.253828562\t383591.60517699\t182292.180510107\t3214\t3163\t6029\t3252\t662133\t490327\t630849\t526600\n+Mir208b\t13.4237202575152\t9.82233816515324\t355.417815392181\t2.80129611458365e-79\t1.06542628891331e-76\t0.124440587141633\t14756\t1245.90702213628\t570.139045385768\t4930.34448733332\t881.902421077918\t0.74532198655141\t0\t0\t0\t2049\t1647\t8904\t2155\t1\t0\t0\t0\n+Mir208a\t11.9775863683342\t8.38828977985358\t348.815401742963\t7.675450754893e-78\t2.18942232783323e-75\t0.0993679816515115\t4638\t433.789589950159\t712.527819143148\t1006.59908044528\t649.748467524829\t0\t0\t0\t0.553722426699609\t1060\t956\t1693\t928\t0\t0\t0\t1\n+Mir499\t14.4882160574998\t8.61277040381698\t291.127944921827\t2.82350748745294e-65\t6.4432440863676e-63\t0.134816198797062\t6527\t608.439028317971\t506.657690265579\t2521.60879492395\t270.357373677161\t0\t0\t0\t0\t869\t730\t4147\t781\t0\t0\t0\t0\n+Mir149\t6.86973108218652\t8.78566474384905\t253.019861795716\t5.70293016120625e-57\t1.08450721898939e-54\t0.0983468375157501\t6164\t774.657674952754\t459.571424069838\t1710.51395913549\t766.394692672161\t17.5039996639232\t6.24646467450714\t4.86444908593961\t5.5386913941544\t1399\t1123\t2295\t1289\t25\t9\t8\t16\n+Mir490\t8.4539298899245\t6.90959613094456\t251.056095815646\t1.52828085290668e-56\t2.4910977902379e-54\t0.0974500488770791\t1741\t209.881556643346\t217.749755819205\t520.538722875595\t195.794075709069\t1.03850463640395\t0.553722426699609\t0\t0.74532198655141\t353\t311\t750\t322\t3\t1\t0\t1\n+Mir802\t-12.4996776940066\t6.62939088571757\t237.561606597444\t1.33781241656995e-53\t1.90805495913289e-51\t0.10939980863872\t1514\t0\t0\t0\t0\t305.654779538184\t164.10342034907\t155.772295189245\t209.286991327076\t0\t0\t0\t0\t552\t401\t209\t352\n+Mir204\t7.37117920479641\t7.55899555710097\t237.12302218121\t1.66736458270285e-53\t2.11384776540439e-51\t0.10292005004102\t2601\t425.578854320855\t326.416358632286\t646.247667592045\t375.481932100929\t3.04028067871226\t0.6923364242693\t0.553722426699609\t3.68311915995418\t571\t549\t923\t541\t5\t2\t1\t9\n+Mir1948\t-7.58332571104735\t7.29345576009458\t204.796406017043\t1.87589722530299e-46\t2.14039873407072e-44\t0.118339985035871\t2404\t1.2161122714849\t0.6923364242693\t1.66116728009883\t1.63694184886853\t647.684806313175\t385.278324943026\t181.341436518244\t428.229856018989\t2\t2\t3\t4\t869\t648\t259\t617\n+Mir3073\t-11.7485555893732\t5.88146234349958\t200.033500954155\t2.05362547312175e-45\t2.13016969530174e-43\t0.110685621278186\t904\t0\t0\t0\t0\t207.347142288176\t75.4646702453536\t72.5376378976488\t87.5763889144661\t0\t0\t0\t0\t341\t218\t131\t214\n+Mir194-2\t-5.43982669183809\t7.86004832737241\t165.57'..b'0.00330101054142751\t0.954183212529461\t0.967174636846159\t0.252311230579068\t8\t0\t0.34616821213465\t1.10744485339922\t0.409235462217131\t0.74532198655141\t0.594565316270102\t0.700159986556928\t0.694051630500793\t0\t1\t2\t1\t1\t1\t1\t1\n+Gm15545\t0.0849589739751836\t-1.89448493270386\t0.0032612312701028\t0.954459808140908\t0.967174636846159\t0.638146949527696\t4\t0\t0.594565316270102\t0.700159986556928\t0\t0.608056135742452\t0\t0.553722426699609\t0\t0\t1\t1\t0\t1\t0\t1\t0\n+Plscr3\t0.0814004336200907\t-1.89261335490638\t0.00301642056831319\t0.956200644868514\t0.968047332759487\t0.638146949527696\t4\t0\t0.74532198655141\t0.594565316270102\t0\t0.694051630500793\t0.608056135742452\t0\t0\t0\t1\t1\t0\t1\t1\t0\t0\n+5430402O13Rik\t-0.0927467442781055\t-1.94142512096775\t0.00279115036404498\t0.957866291573585\t0.968047332759487\t0.638146949527696\t4\t0\t0\t1.2161122714849\t0\t0\t0\t0\t1.1891306325402\t0\t0\t2\t0\t0\t0\t0\t2\n+Gm6297\t-0.0927467442781055\t-1.94142512096775\t0.00279115036404498\t0.957866291573585\t0.968047332759487\t0.638146949527696\t4\t0\t0\t0.818470924434263\t0\t0\t0\t0\t1.2161122714849\t0\t0\t2\t0\t0\t0\t0\t2\n+Gm5095\t0.0741497349563809\t-1.89982855309554\t0.00255353302993466\t0.959698055373646\t0.969040248833035\t0.638146949527696\t4\t0.409235462217131\t0\t0.594565316270102\t0\t0.694051630500793\t0\t0.34616821213465\t0\t1\t0\t1\t0\t1\t0\t1\t0\n+Mir18\t-0.0321144919271105\t2.13829995459641\t0.00222894649578897\t0.96234448681064\t0.970853279797471\t0.319997109480565\t62\t4.9011199058985\t4.85836141350555\t4.86444908593961\t2.42317748494255\t3.87605698689727\t3.68311915995418\t2.98128794620564\t7.72934911151132\t7\t7\t8\t7\t7\t9\t4\t13\n+4930547E14Rik\t0.0332717629837295\t-1.87681159162927\t0.000628960971966741\t0.979991875252521\t0.987622213297045\t0.638146949527696\t4\t0\t0\t0.608056135742452\t0.34616821213465\t0\t0\t0\t1.1891306325402\t0\t0\t1\t1\t0\t0\t0\t2\n+Mir30a\t-0.00674515544774862\t15.2305157438047\t0.000585365330948662\t0.980697605315997\t0.987622213297045\t0.0746707420324099\t565907\t22165.4203400665\t38322.2205825139\t68810.8277478877\t37443.855921078\t63416.8855821185\t38709.4616575002\t22770.252657793\t38928.9014866893\t54163\t51417\t115733\t53479\t91372\t63661\t65778\t70304\n+2610002J02Rik\t0.018998702253143\t-1.31967503888113\t0.000345631121349221\t0.985167257251054\t0.991248536616801\t0.365725430522663\t6\t0\t0\t1.38810326100159\t0.608056135742452\t0.34616821213465\t0.553722426699609\t0.409235462217131\t0\t0\t0\t2\t1\t1\t1\t1\t0\n+Mir1306\t0.010990964703492\t0.387899924622603\t0.000182949792714382\t0.989208227531673\t0.993710996805651\t0.374307689020903\t20\t0.34616821213465\t0.553722426699609\t2.45541277330279\t1.49064397310282\t2.37826126508041\t1.40031997311386\t1.38810326100159\t1.2161122714849\t1\t1\t6\t2\t4\t2\t2\t2\n+2810001G20Rik\t0.0139659525352028\t-1.99687003375001\t0.000177958964401981\t0.989356435031744\t0.993710996805651\t0.638146949527696\t4\t0\t0\t1.40031997311386\t0\t1.2161122714849\t0\t0\t0\t0\t0\t2\t0\t2\t0\t0\t0\n+Snora31\t-0.00608992937342303\t4.51111691273084\t0.000131880843156296\t0.990837344181505\t0.994323139587597\t0.245986767999803\t320\t26.6060794891633\t26.3739619590301\t21.8900208867283\t12.1158874247127\t31.5621783218777\t4.09235462217131\t60.3710809106642\t14.8641329067525\t38\t38\t36\t35\t57\t10\t81\t25\n+2010320M18Rik\t-0.0135816064033237\t-0.577688977281378\t9.37664770823687e-05\t0.992273957831848\t0.994889794276045\t0.436705588816395\t10\t0\t0\t1.03850463640395\t1.10744485339922\t0.409235462217131\t1.49064397310282\t0.594565316270102\t0.700159986556928\t0\t0\t3\t2\t1\t2\t1\t1\n+2310001K24Rik\t0.00612441798475525\t-1.86264950933858\t6.95515125732626e-05\t0.993345915420738\t0.995090157590046\t0.638146949527696\t4\t0\t0\t0.594565316270102\t0.700159986556928\t0\t0.608056135742452\t0.34616821213465\t0\t0\t0\t1\t1\t0\t1\t1\t0\n+Mir1966\t0.000918355090882732\t-0.94191710317151\t1.38947096530728e-05\t0.997025843661245\t0.997900427734632\t0.449008936327196\t8\t0\t0.34616821213465\t1.66116728009883\t0\t1.49064397310282\t0.594565316270102\t0.700159986556928\t0\t0\t1\t3\t0\t2\t1\t1\t0\n+Mir376b\t-0.00136357255892604\t1.39148339025352\t2.78221370209053e-06\t0.998669131632702\t0.998669131632702\t0.592374698826143\t42\t1.49064397310282\t2.37826126508041\t7.70175985212621\t2.08215489150238\t9.72889817187923\t1.73084106067325\t0.553722426699609\t0\t2\t4\t11\t3\t16\t5\t1\t0\n' |
b |
diff -r 643164729057 -r 91e77df18a7f rgedgeR/test-data/gentestdata.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/test-data/gentestdata.sh Fri Jul 26 22:04:58 2013 -0400 |
b |
@@ -0,0 +1,9 @@ +#!/bin/bash +# generate test data for rgGSEA +# ross lazarus June 2013 +# adjust gseajar_path ! +GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar +python ../rgGSEA.py --input_tab "gsea_test_DGE.xls" --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" +--title "GSEA test" --builtin_gmt "gseatestdata.gmt" + + |
b |
diff -r 643164729057 -r 91e77df18a7f rgedgeR/test-data/test_bams2mx.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/test-data/test_bams2mx.xls Fri Jul 26 22:04:58 2013 -0400 |
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b'@@ -0,0 +1,3243 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|
b |
diff -r 643164729057 -r 91e77df18a7f rgedgeR/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/tool_dependencies.xml Fri Jul 26 22:04:58 2013 -0400 |
b |
@@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="package_r3" version="3.0.1"> + <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="biocbasics" version="2.12"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="r3" version="3.0.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2','gplots')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> + </actions> + </install> + <readme>Installs some basic bioc packages for the edgeR wrapper + It's clunky but this is the only way I could get anything installed into the package_r3 R + </readme> + </package> +</tool_dependency> |