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rgToolFactory.py rgedgeRpaired.xml.camera rgedgeRpaired_nocamera.xml test-data/edgeRtest1out.html test-data/edgeRtest1out.xls test-data/gentestdata.sh test-data/test_bams2mx.xls tool_dependencies.xml |
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| diff -r 0de946608423 -r d6fbd1cf7768 rgToolFactory.py --- a/rgToolFactory.py Tue Jan 06 02:20:55 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,638 +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-# march 2014\n-# added ghostscript and graphicsmagick as dependencies \n-# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp\n-# errors ensued\n-#\n-# august 2013\n-# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn\n-#\n-# july 2013\n-# added ability to combine images and individual log files into html output\n-# just make sure there\'s a log file foo.log and it will be output\n-# together with all images named like "foo_*.pdf\n-# otherwise old format for html\n-#\n-# January 2013\n-# problem pointed out by Carlos Borroto\n-# added escaping for <>$ - 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 = \'V001.1 March 2014\' \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'..b'he 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- ste = open(self.elog,\'w\')\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=ste,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- ste.close()\n- err = open(self.elog,\'r\').read()\n- if retval <> 0 and err: # problem\n- print >> sys.stderr,err\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">rgToolFactory.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 0de946608423 -r d6fbd1cf7768 rgedgeRpaired.xml.camera --- a/rgedgeRpaired.xml.camera Tue Jan 06 02:20:55 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1084 +0,0 @@\n-<tool id="rgDifferentialCount" name="Differential_Count" version="0.30">\n- <description>models using BioConductor packages</description>\n- <requirements>\n- <requirement type="package" version="2.14">biocbasics</requirement>\n- <requirement type="package" version="3.0.2">r302</requirement>\n- <requirement type="package" version="1.3.18">graphicsmagick</requirement>\n- <requirement type="package" version="9.10">ghostscript</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" --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 comma separated strings to indicate sample labels for (eg) pairing - must be one 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 \'A99,C21,A99,C21\'">\n- <sanitizer>\n- <valid initial="string.letters,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'..b'Preprint.pdf\n-\n-See Also\n-\n-A voom case study is given in the edgeR User\'s Guide.\n-\n-vooma is a similar function but for microarrays instead of RNA-seq.\n-\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 0de946608423 -r d6fbd1cf7768 rgedgeRpaired_nocamera.xml --- a/rgedgeRpaired_nocamera.xml Tue Jan 06 02:20:55 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1069 +0,0 @@\n-<tool id="rgdifferentialcount" name="Differential_Count" version="0.28">\n- <description>models using BioConductor packages</description>\n- <requirements>\n- <requirement type="package" version="3.1.2">R</requirement>\n- <requirement type="package" version="1.3.18">graphicsmagick</requirement>\n- <requirement type="package" version="9.10">ghostscript</requirement> \n- <requirement type="package" version="2.14">biocbasics</requirement>\n- </requirements>\n- \n- <command interpreter="python">\n- rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "Differential_Counts" \n- --output_dir "$html_file.files_path" --output_html "$html_file" --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" force_select="True">\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" force_select="True">\n- </param>\n- <param name="subjectids" type="text" optional="true" size="120" value = ""\n- label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one 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 \'A99,C21,A99,C21\'">\n- <sanitizer>\n- <valid initial="string.letters,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="10" size="3" \n- label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces p'..b'Preprint.pdf\n-\n-See Also\n-\n-A voom case study is given in the edgeR User\'s Guide.\n-\n-vooma is a similar function but for microarrays instead of RNA-seq.\n-\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 0de946608423 -r d6fbd1cf7768 test-data/edgeRtest1out.html --- a/test-data/edgeRtest1out.html Tue Jan 06 02:20:55 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,621 +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://getgalaxy.org/" /> \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 "Differential_Counts" run at 28/12/2014 21:02:37</div><br/>\n-<div class="toolFormTitle">DESeq2 images and outputs</div>\n-(Click on a thumbnail image to download the corresponding original PDF image)<br/>\n-<div><table class="simple" cellpadding="2" cellspacing="2">\n-<tr>\n-<td><a href="DESeq2_edgeRtest_MA_plot.pdf"><img src="DESeq2_edgeRtest_MA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_MA_plot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_edgeRtest_MA_plot.pdf"/></a></td>\n-\n-<td><a href="DESeq2_edgeRtest_PCA_plot.pdf"><img src="DESeq2_edgeRtest_PCA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_PCA_plot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_edgeRtest_PCA_plot.pdf"/></a></td>\n-\n-<td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf"><img src="DESeq2_edgeRtest_dispersion_estimates.png" title="Click to download a PDF of DESeq2_edgeRtest_dispersion_estimates.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_edgeRtest_dispersion_estimates.pdf"/></a></td>\n-</tr>\n-<tr>\n-<td><a href="DESeq2_edgeRtest_qqplot.pdf"><img src="DESeq2_edgeRtest_qqplot.png" title="Click to download a PDF of DESeq2_edgeRtest_qqplot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_edgeRtest_qqplot.pdf"/></a></td>\n-\n-<td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf"><img src="DESeq2_edgeRtest_sample_distance_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_sample_distance_plot.pdf" hspace="5" width="400" \n- alt="Image called DESeq2_edgeRtest_sample_distance_plot.pdf"/></a></td>\n-\n-<td> </td>\n-</tr></table></div>\n-\n-<div class="toolFormTitle">DESeq2 log output</div>\n-\n-<pre>\n-\n-# DESeq top 50\n-\n- Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL\n-\n-Mir192 Mir192 271352.97636 6.965264 0.2150593 32.387646 4.096935e-230 3.818343e-227 2325567 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir192\'>Mir192</a>\n-\n-Mir122a Mir122a 10112.31117 10.312083 0.3292695 31.318061 2.649329e-215 1.234587e-212 90428 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir122a\'>Mir122a</a>\n-\n-Mir149 Mir149 810.35429 -6.911118 0.2341392 -29.517132 1.735536e-191 5.391733e-189 6164 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir149\'>Mir149</a>\n-\n-Mir23a Mir23a 1289.18043 -3.104086 0.1191688 -26.047815 1.424245e-149 3.318491e-147 10118 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir23a\'>Mir23a</a>\n-\n-Mir181d Mir181d 275.22797 -3.581172 0.1778187 -20.139461 3.329373e-90 6.205952e-88 2139 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir181d\'>Mir181d</a>\n-\n-Mir204 Mir204 347.57397 -7.284200 0.3771119 -19.315751 3.959346e-83 6.150183e-81 2601 <a href=\'http://www.genecards.org/index.php?path=/Search/keyword/Mir204\'>Mir204</a>\n-\n-Mir23b Mir23b 2028.55377 '..b'_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=en_AU.UTF-8 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] parallel splines methods stats graphics grDevices utils datasets base \n-\n-other attached packages:\n-\n- [1] RColorBrewer_1.0-5 DESeq2_1.2.10 RcppArmadillo_0.4.400.0 Rcpp_0.11.2 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 BiocGenerics_0.8.0 edgeR_3.4.2 limma_3.18.13 gplots_2.15.0 stringr_0.6.2 \n-\n-loaded via a namespace (and not attached):\n-\n- [1] annotate_1.40.1 AnnotationDbi_1.24.0 Biobase_2.22.0 bitops_1.0-6 caTools_1.17.1 DBI_0.3.0 gdata_2.13.3 genefilter_1.44.0 grid_3.0.2 gtools_3.4.1 KernSmooth_2.23-13 lattice_0.20-29 locfit_1.5-9.1 RSQLite_0.11.4 stats4_3.0.2 survival_2.37-7 XML_3.98-1.1 xtable_1.7-4 \n-\n-\n-</pre>\n-\n-<div class="toolFormTitle">All output files available for downloading</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="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr>\n-<tr class="odd_row"><td><a href="DESeq2_edgeRtest_MA_plot.pdf">DESeq2_edgeRtest_MA_plot.pdf</a></td><td>15.0 KB</td></tr>\n-<tr><td><a href="DESeq2_edgeRtest_PCA_plot.pdf">DESeq2_edgeRtest_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>\n-<tr class="odd_row"><td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf">DESeq2_edgeRtest_dispersion_estimates.pdf</a></td><td>190.6 KB</td></tr>\n-<tr><td><a href="DESeq2_edgeRtest_qqplot.pdf">DESeq2_edgeRtest_qqplot.pdf</a></td><td>13.3 KB</td></tr>\n-<tr class="odd_row"><td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf">DESeq2_edgeRtest_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>\n-<tr><td><a href="Differential.log">Differential.log</a></td><td>1.4 KB</td></tr>\n-<tr class="odd_row"><td><a href="Differential_Counts.Rscript">Differential_Counts.Rscript</a></td><td>28.3 KB</td></tr>\n-<tr><td><a href="Differential_Counts_error.log">Differential_Counts_error.log</a></td><td>1.8 KB</td></tr>\n-<tr class="odd_row"><td><a href="Differential_Counts_runner.log">Differential_Counts_runner.log</a></td><td>1.3 KB</td></tr>\n-<tr><td><a href="Differential_rowsum_bar_charts.pdf">Differential_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>\n-<tr class="odd_row"><td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf">Differential_venn_edgeRtest_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>\n-<tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>\n-<tr class="odd_row"><td><a href="VOOM_edgeRtest_mean_variance_plot.pdf">VOOM_edgeRtest_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>\n-<tr><td><a href="VOOM_edgeRtest_qqplot.pdf">VOOM_edgeRtest_qqplot.pdf</a></td><td>17.5 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR.log">edgeR.log</a></td><td>10.4 KB</td></tr>\n-<tr><td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf">edgeR_edgeRtest_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_edgeRtest_GoodnessofFit.pdf">edgeR_edgeRtest_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>\n-<tr><td><a href="edgeR_edgeRtest_MDSplot.pdf">edgeR_edgeRtest_MDSplot.pdf</a></td><td>4.9 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_edgeRtest_qqplot.pdf">edgeR_edgeRtest_qqplot.pdf</a></td><td>15.2 KB</td></tr>\n-<tr><td><a href="edgeR_edgeRtest_smearplot.pdf">edgeR_edgeRtest_smearplot.pdf</a></td><td>16.7 KB</td></tr>\n-<tr class="odd_row"><td><a href="edgeR_edgeRtest_top_100_heatmap.pdf">edgeR_edgeRtest_top_100_heatmap.pdf</a></td><td>11.2 KB</td></tr>\n-</table></div><br/>\n-</div></body></html>\n-\n' |
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| diff -r 0de946608423 -r d6fbd1cf7768 test-data/edgeRtest1out.xls --- a/test-data/edgeRtest1out.xls Tue Jan 06 02:20:55 2015 -0500 +++ /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\tliver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam\tliver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam\theart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam\n-Mir208a\t-11.840750632598\t8.46501715136261\t594.169461743406\t3.10454347546078e-131\t3.54228410550075e-128\t0.0517121951967719\t4638\t0\t0\t0\t0.539638866040004\t789.596577514809\t739.374891373071\t627.962821069374\t673.126883915814\t0\t0\t0\t1\t1060\t956\t1693\t928\n-Mir149\t-7.00898388335376\t8.86176664758882\t484.303208152322\t2.47390942925463e-107\t1.41136532938977e-104\t0.0495993679583824\t6164\t9.41025046314352\t5.51321148265855\t4.26049561369029\t8.63422185664007\t1042.11850183323\t868.533475953932\t851.254975991856\t934.979044577031\t25\t9\t8\t16\t1399\t1123\t2295\t1289\n-Mir208b\t-13.291634767704\t9.90594480087289\t417.69757945293\t7.73746269808422e-93\t2.9428149795047e-90\t0.105080963355037\t14756\t0.376410018525741\t0\t0\t0\t1526.30508238476\t1273.79753775256\t3302.64675652788\t1563.13408926571\t1\t0\t0\t0\t2049\t1647\t8904\t2155\n-Mir122a\t10.5146833711912\t12.4780878408673\t415.174288147205\t2.74052534761176e-92\t7.81734855406255e-90\t0.108038824165009\t90428\t11204.5970214557\t14844.628206585\t6343.34540683313\t13201.1855799366\t8.93882917941294\t5.41383288662291\t10.0147644234336\t5.8028179647915\t29767\t24233\t11911\t24463\t12\t7\t27\t8\n-Mir204\t-7.49816212335945\t7.63450677628189\t341.306784530615\t3.31342972702995e-76\t7.56124663708234e-74\t0.0690795844187195\t2601\t1.8820500926287\t1.22515810725746\t0.532561951711286\t4.85674979436004\t425.339288453732\t424.599179250854\t342.356576401082\t392.415564869025\t5\t2\t1\t9\t571\t549\t923\t541\n-Mir499\t-13.5774541855867\t8.70007828481468\t325.791992848402\t7.93075479822316e-73\t1.50816520412877e-70\t0.120422839295321\t6527\t0\t0\t0\t0\t647.32021307582\t564.58542960496\t1538.19363199923\t566.50010381277\t0\t0\t0\t0\t869\t730\t4147\t781\n-Mir490\t-8.53439419162448\t6.99102321339932\t303.171839764489\t6.71036610165275e-68\t1.0937896745694e-65\t0.0794971090139375\t1741\t1.12923005557722\t0.612579053628728\t0\t0.539638866040004\t262.950558361064\t240.528861105675\t278.187900650933\t233.563423082858\t3\t1\t0\t1\t353\t311\t750\t322\n-Mir192\t6.95385326892851\t17.1693636192881\t217.228665712558\t3.63830691057425e-49\t5.18913523120652e-47\t0.127009948729763\t2325567\t249233.494796504\t300364.049628613\t335966.174675113\t284173.826856666\t2394.11641521943\t2446.27906005547\t2236.25980403264\t2358.84550268775\t662133\t490327\t630849\t526600\t3214\t3163\t6029\t3252\n-Mir802\t11.4408053854897\t6.59338011170441\t212.880585690967\t3.23164416041045e-48\t4.09700665225369e-46\t0.122736709286819\t1514\t207.778330226209\t245.64420050512\t111.305447907659\t189.952880846082\t0\t0\t0\t0\t552\t401\t209\t352\t0\t0\t0\t0\n-Mir1948\t7.41814210388816\t7.25273383973858\t195.669583337086\t1.84024810781419e-44\t2.09972309101599e-42\t0.120602206144644\t2404\t327.100306098869\t396.951226751416\t137.933545493223\t332.957180346683\t1.48980486323549\t1.54680939617797\t1.11275160260373\t2.90140898239575\t869\t648\t259\t617\t2\t2\t3\t4\n-Mir194-2\t5.29895000039034\t7.81152218291727\t191.855876444429\t1.25095991572432e-43\t1.29758660349223e-41\t0.0867075108859984\t3570\t495.355584379875\t529.88088138885\t233.794696801255\t474.882202115204\t14.1531462007372\t11.6010704713348\t7.41834401735823\t11.605635929583\t1316\t865\t439'..b'73498972596457\t0.00166750535258586\t0.967427357317129\t0.979600222217201\t0.367416862910588\t9\t0.376410018525741\t0\t1.06512390342257\t1.07927773208001\t0.744902431617745\t1.54680939617797\t0\t0.725352245598938\t1\t0\t2\t2\t1\t2\t0\t1\n-6330549D23Rik\t0.0365504895754985\t0.766481265149971\t0.00165505138189159\t0.967549154353767\t0.979600222217201\t0.144795356612801\t9\t0.752820037051481\t1.22515810725746\t0\t0.539638866040004\t0.744902431617745\t0.773404698088987\t0.370917200867911\t0.725352245598938\t2\t2\t0\t1\t1\t1\t1\t1\n-Gm16291\t-0.0497984136905431\t1.04049827004916\t0.00165184486677905\t0.96758058758877\t0.979600222217201\t0.760533853439203\t14\t0.752820037051481\t0.612579053628728\t2.66280975855643\t0\t2.23470729485323\t1.54680939617797\t0\t0.725352245598938\t2\t1\t5\t0\t3\t2\t0\t1\n-Gm4890\t-0.0259416163380367\t0.436081268353407\t0.00151936462515234\t0.968907109122493\t0.98007359176309\t0.663367644323302\t4\t0\t0\t1.06512390342257\t0\t0\t0\t0.741834401735823\t0\t0\t0\t2\t0\t0\t0\t2\t0\n-5430402O13Rik\t-0.0215659699049333\t0.436296133284018\t0.00131072419039668\t0.971119756290488\t0.980573134449068\t0.66336084861507\t4\t0\t0\t0\t1.07927773208001\t0\t0\t0.741834401735823\t0\t0\t0\t0\t2\t0\t0\t2\t0\n-Gm6297\t-0.0215659699049333\t0.436296133284018\t0.00131072419039668\t0.971119756290488\t0.980573134449068\t0.66336084861507\t4\t0\t0\t0\t1.07927773208001\t0\t0\t0.741834401735823\t0\t0\t0\t0\t2\t0\t0\t2\t0\n-G730013B05Rik\t-0.0385365765720963\t1.01651726367811\t0.000926357662148547\t0.975719235170337\t0.983633409630645\t0.703663961483763\t14\t2.25846011115444\t0\t1.06512390342257\t0\t1.48980486323549\t1.54680939617797\t0.741834401735823\t0\t6\t0\t2\t0\t2\t2\t2\t0\n-Fut8\t-0.0301535765572007\t0.983272857012977\t0.000914530335813346\t0.975874688608142\t0.983633409630645\t0.461988777734778\t13\t0.376410018525741\t0.612579053628728\t2.66280975855643\t0\t0.744902431617745\t1.54680939617797\t0.741834401735823\t0.725352245598938\t1\t1\t5\t0\t1\t2\t2\t1\n-Mir451\t0.00783986907310383\t10.6424503554937\t0.000668429572201035\t0.979373786499111\t0.986289047127525\t0.0880041428130113\t23834\t1259.46792198713\t1282.12795924493\t1240.8693474873\t2624.26380555254\t1712.5306902892\t1143.86554847361\t1957.70098618084\t1556.60591905532\t3346\t2093\t2330\t4863\t2299\t1479\t5278\t2146\n-Mir3103\t-0.0011092316730465\t0.437273490728585\t0.00054275250380531\t0.981413325432899\t0.987471432380016\t0.663329937374097\t4\t0\t0.612579053628728\t0\t0.539638866040004\t0\t0\t0.741834401735823\t0\t0\t1\t0\t1\t0\t0\t2\t0\n-Mir877\t0.0169238059397901\t2.07117778204749\t0.000493226392977775\t0.982281477037185\t0.987474154448835\t0.411290532451564\t45\t2.25846011115444\t4.2880533754011\t0.532561951711286\t5.93602752644005\t2.23470729485323\t3.09361879235595\t1.85458600433956\t5.8028179647915\t6\t7\t1\t11\t3\t4\t5\t8\n-Mirlet7a-2\t0.00692268187132084\t3.52904314853656\t0.000229292382525781\t0.987918571764677\t0.991638607573432\t0.145210168895582\t158\t13.1743506484009\t10.4138439116884\t7.98842927566929\t9.71349958872008\t8.93882917941294\t9.28085637706784\t13.7239364321127\t8.70422694718725\t35\t17\t15\t18\t12\t12\t37\t12\n-Adarb1\t-0.0208372088988242\t1.01574105327976\t0.000220136486121625\t0.988162223322517\t0.991638607573432\t0.682420434692774\t14\t2.25846011115444\t0\t1.06512390342257\t0\t1.48980486323549\t0\t0.741834401735823\t1.45070449119788\t6\t0\t2\t0\t2\t0\t2\t2\n-Zfp821\t0.0194908209613808\t0.438251386312134\t0.000105716899237329\t0.991796397330917\t0.994410974828274\t0.663299009834018\t4\t0\t1.22515810725746\t0\t0\t0\t0\t0.741834401735823\t0\t0\t2\t0\t0\t0\t0\t2\t0\n-Snord7\t-0.00363412912961608\t0.808396104681926\t2.65747690626483e-05\t0.99588686572452\t0.997635569615169\t1.23423123101037\t10\t2.25846011115444\t0\t0\t0\t0.744902431617745\t0\t0.370917200867911\t1.45070449119788\t6\t0\t0\t0\t1\t0\t1\t2\n-D330022K07Rik\t8.83246306215062e-05\t2.3059219632559\t9.35429808279764e-07\t0.999228305160102\t0.999852120027929\t0.587915295555401\t56\t4.89333024083463\t0.612579053628728\t9.05355317909186\t1.07927773208001\t4.46941458970647\t7.73404698088987\t1.11275160260373\t2.90140898239575\t13\t1\t17\t2\t6\t10\t3\t4\n-AA465934\t-0.00551213095838715\t1.05434721413031\t3.43509380940077e-08\t0.999852120027929\t0.999852120027929\t1.50064027311007\t15\t3.38769016673167\t0\t0\t0\t0.744902431617745\t0\t0.741834401735823\t2.17605673679681\t9\t0\t0\t0\t1\t0\t2\t3\n' |
| b |
| diff -r 0de946608423 -r d6fbd1cf7768 test-data/gentestdata.sh --- a/test-data/gentestdata.sh Tue Jan 06 02:20:55 2015 -0500 +++ /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 0de946608423 -r d6fbd1cf7768 test-data/test_bams2mx.xls --- a/test-data/test_bams2mx.xls Tue Jan 06 02:20:55 2015 -0500 +++ /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 0de946608423 -r d6fbd1cf7768 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 06 02:20:55 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,62 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="3.1.2"> - <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="ghostscript" version="9.10"> - <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - - <package name="biocbasics" version="2.14"> - <install version="1.0"> - <actions> - <action type="setup_r_environment"> - <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="R" version="3.1.2" /> - </repository> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/survival_2.37-7.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/lars_1.2.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/lattice_0.20-29.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/latticeExtra_0.6-26.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Matrix_1.1-4.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/glmnet_1.9-8.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/KernSmooth_2.23-13.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/numDeriv_2012.9-1.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/lava_1.3.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/prodlim_1.5.1.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/codetools_0.2-9.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/iterators_1.0.7.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreach_1.4.2.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Formula_1.1-2.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.1-2.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/cluster_1.15.3.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rpart_4.1-8.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/nnet_7.3-8.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/acepack_1.3-3.3.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreign_0.8-61.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Hmisc_3.14-6.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/SparseM_1.05.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/quantreg_5.05.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/nlme_3.1-118.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/polspline_1.1.9.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/mvtnorm_1.0-2.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/TH.data_1.0-5.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/zoo_1.7-11.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/sandwich_2.3-2.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/multcomp_1.3-8.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rms_4.2-1.tar.gz?raw=true</package> - <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/pec_2.4.4.tar.gz?raw=true</package> - - </action> - </actions> - </install> - <readme> - Differential gene expression analysis - You may need libxml2-dev for XML to compile - Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so - </readme> - </package> -</tool_dependency> |