| Previous changeset 53:9cbc5a72fc3f (2013-07-26) |
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Commit message:
Deleted selected files |
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removed:
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 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/rgToolFactory.py --- a/rgedgeR/rgToolFactory.py Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,599 +0,0 @@\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 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/rgedgeRpaired.xml --- a/rgedgeR/rgedgeRpaired.xml Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,867 +0,0 @@\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">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="doDESeq2'..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 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/test-data/edgeRtest1out.html --- a/rgedgeR/test-data/edgeRtest1out.html Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,813 +0,0 @@\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 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/test-data/edgeRtest1out.xls --- a/rgedgeR/test-data/edgeRtest1out.xls Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1142 +0,0 @@\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 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/test-data/gentestdata.sh --- a/rgedgeR/test-data/gentestdata.sh Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -#!/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 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/test-data/test_bams2mx.xls --- a/rgedgeR/test-data/test_bams2mx.xls Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,3243 +0,0 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Zfp672\t0\t0\t0\t0\t0\t2\t0\t0\n-Zfp783\t0\t0\t0\t0\t0\t0\t0\t0\n-Zfp809\t7\t1\t0\t0\t0\t4\t2\t0\n-Zfp821\t0\t0\t0\t2\t2\t0\t0\t0\n-Zfp862\t4\t0\t0\t0\t0\t10\t2\t0\n-Zim3\t0\t0\t0\t0\t0\t0\t0\t0\n-Zmynd8\t3\t5\t4\t4\t3\t8\t2\t1\n-Znf41-ps\t0\t0\t0\t0\t0\t0\t0\t0\n-Zp4-ps\t0\t0\t0\t0\t0\t0\t0\t0\n-Zscan4a\t0\t0\t0\t0\t0\t0\t0\t0\n-Zxda\t0\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 9cbc5a72fc3f -r b1d6dae9c309 rgedgeR/tool_dependencies.xml --- a/rgedgeR/tool_dependencies.xml Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="r3" version="3.0.1"> - <repository changeset_revision="6e89ec508745" 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="6e89ec508745" 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')" >> $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 "install.packages(c('stringr','gplots'),dependencies=T)" >> $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> |