Galaxy |

Changeset 0:33f04fc1f109 (2018-04-26)

Commit message:
Uploaded

added:
RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.py
RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.xml
RemovingNonAsciicharsfromtextfile/test-data/RemovingNonAsciicharsfromtextfile_test1_input.xls
RemovingNonAsciicharsfromtextfile/test-data/RemovingNonAsciicharsfromtextfile_test1_output.xls
RemovingNonAsciicharsfromtextfile/test-data/test1_out.log

diff -r 000000000000 -r 33f04fc1f109 RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.py Thu Apr 26 10:57:25 2018 -0400

[

b'@@ -0,0 +1,742 @@\n+# RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py\n+# to make a new Galaxy tool called RemovingNonAsciicharsfromtextfile\n+# User pela@centrum.cz at 26/04/2018 16:33:36\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+# August 2014 \n+# merged John Chilton\'s citation addition and ideas from Marius van den Beek to enable arbitrary\n+# data types for input and output - thanks!\n+#\n+# march 2014\n+# had to remove dependencies because cross toolshed dependencies are not possible - can\'t pre-specify a toolshed url for graphicsmagick and ghostscript\n+# grrrrr - night before a demo\n+# added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable\n+#\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 '..b'nterpreter)\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,\'a\')\n+ sto = open(self.tlog,\'a\')\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\').readlines()\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">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=\'./\')\n+ a(\'--output_html\',default=None)\n+ a(\'--input_tab\',default="None")\n+ a(\'--input_formats\',default="tabular,text")\n+ a(\'--output_tab\',default="None")\n+ a(\'--output_format\',default="tabular")\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(\'--citations\',default=None)\n+ a(\'--tool_desc\',default=None)\n+ a(\'--new_tool\',default=None)\n+ a(\'--tool_version\',default=None)\n+ a(\'--include_dependencies\',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+\n'

diff -r 000000000000 -r 33f04fc1f109 RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RemovingNonAsciicharsfromtextfile/RemovingNonAsciicharsfromtextfile.xml Thu Apr 26 10:57:25 2018 -0400

[

@@ -0,0 +1,68 @@
+<tool id="RemovingNonAsciicharsfromtextfile" name="RemovingNonAsciicharsfromtextfile" version="0.01">
+<description>Removing Non-Ascii chars from text file</description>
+
+<command interpreter="python">
+
+        RemovingNonAsciicharsfromtextfile.py --script_path "$runMe" --interpreter "bash"
+            --tool_name "RemovingNonAsciicharsfromtextfile" --input_tab "$input1"   --output_dir "./" --output_tab "$tab_file"
+</command>
+<inputs>
+<param name="input1"  type="data" format="interval,tabular,txt" label="Select a suitable input file from your history"/>
+<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="RemovingNonAsciicharsfromtextfile"/>
+
+</inputs>
+<outputs>
+ <data format="txt" name="tab_file" label="${job_name}"/>
+
+</outputs>
+<configfiles>
+<configfile name="runMe">
+#!/bin/bash
+INF=\$1
+OUTF=\$2
+perl -pe's/[[:^ascii:]]//g' < \$INF > \$OUTF
+</configfile>
+</configfiles>
+
+
+        <tests>
+        <test>
+        <param name="input1" value="RemovingNonAsciicharsfromtextfile_test1_input.xls" ftype="interval,tabular,txt"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="tab_file" file="RemovingNonAsciicharsfromtextfile_test1_output.xls" ftype="txt"/>
+        </test>
+        </tests>
+
+
+<help>
+
+
+**What it Does**
+
+Removing Non-Ascii chars from text file
+
+**Script**
+Pressing execute will run the following code over your input file and generate some outputs in your history::
+
+
+ #!/bin/bash
+ INF=\$1
+ OUTF=\$2
+ perl -pe's/[[:^ascii:]]//g' < \$INF > \$OUTF
+
+**Attribution**
+This Galaxy tool was created by pela@centrum.cz at 26/04/2018 16:33:35
+using the Galaxy Tool Factory.
+
+See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
+Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+
+</help>
+<citations>
+
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+</citations>
+</tool>

diff -r 000000000000 -r 33f04fc1f109 RemovingNonAsciicharsfromtextfile/test-data/RemovingNonAsciicharsfromtextfile_test1_input.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RemovingNonAsciicharsfromtextfile/test-data/RemovingNonAsciicharsfromtextfile_test1_input.xls Thu Apr 26 10:57:25 2018 -0400

b'@@ -0,0 +1,9986 @@\n+#id\tchrom\tinputPos\tinputRef\tinputAlt\tunannotatedReason\tgene\tgeneId\tgeneDesc\ttranscript\tstrand\ttransLen\tcdsLen\tprotein\tUniprot\tvarType\tcodingEffect\tvarLocation\tassembly\tgDNAstart\tgDNAend\tgNomen\tcDNAstart\tcDNAend\tcNomen\tpNomen\talt_pNomen\texon\tintron\tomimId\tdistNearestSS\tnearestSSType\twtSSFScore\twtMaxEntScore\twtNNSScore\twtGSScore\tvarSSFScore\tvarMaxEntScore\tvarNNSScore\tvarGSScore\tnearestSSChange\tlocalSpliceEffect\tlocalSS_pos\tlocalSS_wtMaxEntScore\tlocalSS_wtNNSScore\tlocalSS_wtSSFScore\tlocalSS_varMaxEntScore\tlocalSS_varNNSScore\tlocalSS_varSSFScore\tbranchPointPos\tbranchPointChange\tproteinDomain1\tproteinDomain2\tproteinDomain3\tproteinDomain4\trsId\trsValidated\trsSuspect\trsValidations\trsValidationNumber\trsAncestralAllele\trsHeterozygosity\trsClinicalSignificance\trsMAF\trsMAFAllele\trsMAFCount\t1000g_AF\t1000g_AFR_AF\t1000g_SAS_AF\t1000g_EAS_AF\t1000g_EUR_AF\t1000g_AMR_AF\tgnomadAltFreq_all\tgnomadAltFreq_afr\tgnomadAltFreq_amr\tgnomadAltFreq_asj\tgnomadAltFreq_eas\tgnomadAltFreq_sas\tgnomadAltFreq_nfe\tgnomadAltFreq_fin\tgnomadAltFreq_oth\tgnomadAltFreq_popmax\tgnomadAltCount_all\tgnomadAltCount_afr\tgnomadAltCount_amr\tgnomadAltCount_asj\tgnomadAltCount_eas\tgnomadAltCount_sas\tgnomadAltCount_nfe\tgnomadAltCount_fin\tgnomadAltCount_oth\tgnomadTotalCount_all\tgnomadTotalCount_afr\tgnomadTotalCount_amr\tgnomadTotalCount_asj\tgnomadTotalCount_eas\tgnomadTotalCount_sas\tgnomadTotalCount_nfe\tgnomadTotalCount_fin\tgnomadTotalCount_oth\tgnomadHomFreq_all\tgnomadHomFreq_afr\tgnomadHomFreq_amr\tgnomadHomFreq_asj\tgnomadHomFreq_eas\tgnomadHomFreq_sas\tgnomadHomFreq_nfe\tgnomadHomFreq_fin\tgnomadHomFreq_oth\tgnomadHomCount_all\tgnomadHomCount_afr\tgnomadHomCount_amr\tgnomadHomCount_asj\tgnomadHomCount_eas\tgnomadHomCount_sas\tgnomadHomCount_nfe\tgnomadHomCount_fin\tgnomadHomCount_oth\tgnomadHetCount_all\tgnomadHetCount_afr\tgnomadHetCount_amr\tgnomadHetCount_asj\tgnomadHetCount_eas\tgnomadHetCount_sas\tgnomadHetCount_nfe\tgnomadHetCount_fin\tgnomadHetCount_oth\tgnomadHemCount_all\tgnomadHemCount_afr\tgnomadHemCount_amr\tgnomadHemCount_asj\tgnomadHemCount_eas\tgnomadHemCount_sas\tgnomadHemCount_nfe\tgnomadHemCount_fin\tgnomadHemCount_oth\tgnomadFilter\tgnomadReadDepth\tgnomadOrigin\tespRefEACount\tespRefAACount\tespRefAllCount\tespAltEACount\tespAltAACount\tespAltAllCount\tespEAMAF\tespAAMAF\tespAllMAF\tespEAAAF\tespAAAAF\tespAllAAF\tespAvgReadDepth\tclinVarIds\tclinVarOrigins\tclinVarMethods\tclinVarClinSignifs\tclinVarReviewStatus\tclinVarPhenotypes\thgmdId\thgmdPhenotype\thgmdPubMedId\thgmdSubCategory\tcosmicIds\tcosmicTissues\tcosmicFreqs\tcosmicSampleCounts\tinsNucs\tdelNucs\tsubstType\twtNuc\tvarNuc\tnucChange\tphastCons\tphyloP\twtAA_1\twtAA_3\twtCodon\twtCodonFreq\tvarAA_1\tvarAA_3\tvarCodon\tvarCodonFreq\tposAA\tnOrthos\tconservedOrthos\tconservedDistSpecies\tBLOSUM45\tBLOSUM62\tBLOSUM80\twtAAcomposition\tvarAAcomposition\twtAApolarity\tvarAApolarity\twtAAvolume\tvarAAvolume\tgranthamDist\tAGVGDclass\tAGVGDgv\tAGVGDgd\tSIFTprediction\tSIFTweight\tSIFTmedian\tMAPPprediction\tMAPPpValue\tMAPPpValueMedian\tQUAL\tFILTER\t1000G2012APR_AFR\t1000G2012APR_ALL\t1000G2012APR_AMR\t1000G2012APR_ASN\t1000G2012APR_EUR\t1000G_AFR\t1000G_ALL\t1000G_AMR\t1000G_EAS\t1000G_EUR\t1000G_SAS\tAAChange.ensGene\tAAChange.knownGene\tAAChange.refGene\tAC\tAC3\tAF1\tAFR.sites.2015_08\tALL.sites.2015_08\tALLELE_ORIGIN\tALTCOUNT\tAMR.sites.2015_08\tAN\tANNOVAR_DATE\tBA1\tBP1\tBP2\tBP3\tBP4\tBP5\tBP6\tBP7\tBS1\tBS2\tBS3\tBS4\tCADD\tCADD13_PHRED\tCADD13_RawScore\tCADD_Phred\tCADD_phred\tCADD_raw\tCADD_raw_rankscore\tCG46\tCLINICAL_SIGNIFICANCE\tCLINSIG\tCLNACC\tCLNDBN\tCLNDSDB\tCLNDSDBID\tCategory\tDANN_rankscore\tDANN_score\tDISTANCE\tDP\tDP4\tEAS.sites.2015_08\tEFF\tESP6500si_AA\tESP6500si_ALL\tESP6500si_EA\tESP6500siv2_AA\tESP6500siv2_ALL\tESP6500siv2_EA\tEUR.sites.2015_08\tEigen\tEigen-PC-raw\tEigen-raw\tEigen_coding_or_noncoding\tExAC_AFR\tExAC_ALL\tExAC_AMR\tExAC_EAS\tExAC_FIN\tExAC_Freq\tExAC_NFE\tExAC_OTH\tExAC_SAS\tExAC_nonpsych_AFR\tExAC_nonpsych_ALL\tExAC_nonpsych_AMR\tExAC_nonpsych_EAS\tExAC_nonpsych_FIN\tExAC_nonpsych_NFE\tExAC_nonpsych_OTH\tExAC_nonpsych_SAS\tExAC_nontcga_AFR\tExAC_nontcga_ALL\tExAC_nontcga_AMR\tExAC_nontcga_EAS\tExAC_nontcga_FIN\tExAC_nontcga_NFE\tExAC'..b'\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+rs2974804 (chrY:59355957 G/A)\tY\t59355957\tG\tA\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+rs3953915 (chrY:59357787 G/A)\tY\t59357787\tG\tA\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+. (chrY:59359427 T/A)\tY\t59359427\tT\tA\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+. (chrY:59359458 A/G)\tY\t59359458\tA\tG\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+. (chrY:59359459 A/G)\tY\t59359459\tA\tG\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+rs778058786 (chrY:59359945 C/T)\tY\t59359945\tC\tT\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n+rs371319796 (chrY:59359978 C/T)\tY\t59359978\tC\tT\tNot on a known gene\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\n'

diff -r 000000000000 -r 33f04fc1f109 RemovingNonAsciicharsfromtextfile/test-data/RemovingNonAsciicharsfromtextfile_test1_output.xls
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RemovingNonAsciicharsfromtextfile/test-data/RemovingNonAsciicharsfromtextfile_test1_output.xls Thu Apr 26 10:57:25 2018 -0400

diff -r 000000000000 -r 33f04fc1f109 RemovingNonAsciicharsfromtextfile/test-data/test1_out.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/RemovingNonAsciicharsfromtextfile/test-data/test1_out.log Thu Apr 26 10:57:25 2018 -0400

@@ -0,0 +1,1 @@
+## Toolfactory generated command line = bash /home/lab/galaxy/galaxy/database/tmp/RemovingNonAsciicharsfromtextfilexVIx7q.bash /home/lab/galaxy/galaxy/database/files/000/dataset_27.dat /home/lab/galaxy/galaxy/database/files/000/dataset_31.dat