| Next changeset 1:d1c88b118a3f (2015-03-13) |
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Commit message:
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added:
ffp_macros.xml ffp_phylogeny.py ffp_phylogeny.xml tarballit.sh test-data/genome1 test-data/genome2 test-data/test_length_1_output.tabular test-data/test_length_2_output.tabular tool_dependencies.xml |
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| diff -r 000000000000 -r eb6e5e78a066 ffp_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ffp_macros.xml Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,21 @@ +<macros> + + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + + <xml name="requirements"> + <requirements> + <requirement type="binary">@BINARY@</requirement> + </requirements> + <version_command interpreter="python">@BINARY@ --version</version_command> + </xml> + +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r eb6e5e78a066 ffp_phylogeny.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ffp_phylogeny.py Mon Feb 23 18:25:25 2015 -0500 |
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| b'@@ -0,0 +1,353 @@\n+#!/usr/bin/python\n+import optparse\n+import time\n+import os\n+import tempfile\n+import sys\n+import shlex, subprocess\n+from string import maketrans\n+\n+VERSION_NUMBER = "0.1.00"\n+\n+class MyParser(optparse.OptionParser):\n+\t"""\n+\t From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output\n+\t Provides a better class for displaying formatted help info in epilog() portion of optParse; allows for carriage returns.\n+\t"""\n+\tdef format_epilog(self, formatter):\n+\t\treturn self.epilog\n+\n+\n+def stop_err( msg ):\n+ sys.stderr.write("%s\\n" % msg)\n+ sys.exit(1)\n+\n+def getTaxonomyNames(type, multiple, abbreviate, filepaths, filenames):\n+\t"""\n+\tReturns a taxonomic list of names corresponding to each file being analyzed by ffp.\n+\tThis may also include names for each fasta sequence found within a file if the\n+\t"-m" multiple option is provided. \tDefault is to use the file names rather than fasta id\'s inside the files.\n+\tNOTE: THIS DOES NOT (MUST NOT) REORDER NAMES IN NAME ARRAY. \n+\tEACH NAME ENTRY IS TRIMMED AND MADE UNIQUE\n+\t\n+\t@param type string [\'text\',\'amino\',\'nucleotide\']\n+\t@param multiple boolean Flag indicates to look within files for labels\n+\t@param abbreviate boolean Flag indicates to shorten labels\t\n+\t@filenames array original input file names as user selected them\n+\t@filepaths array resulting galaxy dataset file .dat paths\n+\t\n+\t"""\n+\t# Take off prefix/suffix whitespace/comma :\n+\ttaxonomy = filenames.strip().strip(\',\').split(\',\')\n+\ttranslations = maketrans(\' .-\t\',\'____\')\n+\tnames=[]\n+\tptr = 0\n+\n+\tfor file in filepaths:\n+\t\t# First, convert space, period to underscore in file names.\t ffprwn IS VERY SENSITIVE ABOUT THIS.\n+\t\t# Also trim labels to 50 characters. Turns out ffpjsd is kneecapping a taxonomy label to 10 characters if it is greater than 50 chars.\n+\t\ttaxonomyitem = taxonomy[ptr].strip().translate(translations)[:50]\n+\t\t# print taxonomyitem\n+\t\tif not type in \'text\' and multiple:\n+\t\t\t#Must read each fasta file, looking for all lines beginning ">"\n+\t\t\twith open(file) as fastafile:\n+\t\t\t\tlineptr = 0\n+\t\t\t\tfor line in fastafile:\n+\t\t\t\t\tif line[0] == \'>\':\n+\t\t\t\t\t\tname = line[1:].split(None,1)[0].strip()[:50]\n+\t\t\t\t\t\t# Odd case where no fasta description found\n+\t\t\t\t\t\tif name == \'\': name = taxonomyitem + \'.\' + str(lineptr)\n+\t\t\t\t\t\tnames.append(name)\n+\t\t\t\t\t\tlineptr += 1\n+\t\telse:\n+\t\t\tnames.append(taxonomyitem)\n+\t\t\n+\t\tptr += 1\n+\n+\tif abbreviate:\n+\t\tnames = trimCommonPrefixes(names)\n+\t\tnames = trimCommonPrefixes(names, True) # reverse = Suffixes.\n+\n+\treturn names\n+\t\n+def trimCommonPrefixes(names, reverse=False):\n+\t"""\n+\tExamines sorted array of names. Trims off prefix of each subsequent pair.\n+\t\n+\t@param names array of textual labels (file names or fasta taxonomy ids)\n+\t@param reverse boolean whether to reverse array strings before doing prefix trimming.\n+\t"""\n+\twordybits = \'|.0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ\'\n+\n+\tif reverse:\n+\t\tnames = map(lambda name: name[::-1], names) #reverses characters in names\n+\t\n+\tsortednames = sorted(names)\n+\tptr = 0\n+\tsortedlen = len(sortednames)\n+\toldprefixlen=0\n+\tprefixlen=0\n+\tfor name in sortednames:\n+\t\tptr += 1\n+\n+\t\t#If we\'re not at the very last item, reevaluate prefixlen\n+\t\tif ptr < sortedlen:\n+\n+\t\t\t# Skip first item in an any duplicate pair. Leave duplicate name in full.\n+\t\t\tif name == sortednames[ptr]:\n+\t\t\t\tif reverse:\n+\t\t\t\t\tcontinue\n+\t\t\t\telse:\n+\t\t\t\t\tnames[names.index(name)] = \'DupLabel-\' + name\n+\t\t\t\t\tcontinue\n+\n+\t\t\t# See http://stackoverflow.com/questions/9114402/regexp-finding-longest-common-prefix-of-two-strings\n+\t\t\tprefixlen = len( name[:([x[0]==x[1] for x in zip(name, sortednames[ptr])]+[0]).index(0)] )\n+\t\t\t\t\n+\t\tif prefixlen <= oldprefixlen:\n+\t\t\tnewprefix = name[:oldprefixlen]\n+\t\telse:\n+\t\t\tnewprefix = name[:prefixlen]\n+\t\t# Expands label to include any preceeding characters that were probably part of it.\n+\t\tnewprefix = newprefix.rstrip(wordybits)\n+\t\tnewname = name[len(newprefix):]\n+\t\t# Some tree visualizers '..b'al category (protein or purine/pyrimidine group) before being counted. Disable this to treat individual characters as distinct.\')\n+\n+\t\tparser.add_option(\'-a\', \'--abbreviate\', dest=\'abbreviate\', default=False, action=\'store_true\', \n+\t\t\thelp=\'Shorten tree taxonomy labels as much as possible.\')\n+\t\t\n+\t\tparser.add_option(\'-s\', \'--similarity\', dest=\'similarity\', default=False, action=\'store_true\', \n+\t\t\thelp=\'Enables pearson correlation coefficient matrix and any of the binary distance measures to be turned into similarity matrixes.\')\n+\t\t\n+\t\tparser.add_option(\'-f\', \'--filter\', type=\'choice\', dest=\'filter\', default=\'none\',\n+\t\t\tchoices=[\'none\',\'f\',\'n\',\'e\',\'freq\',\'norm\',\'evd\'],\n+\t\t\thelp=\'Choice of [f=raw frequency|n=normal|e=extreme value (Gumbel)] distribution: Features are trimmed from the data based on lower/upper cutoff points according to the given distribution.\')\n+\n+\t\tparser.add_option(\'-L\', \'--lower\', type=\'float\', dest=\'lower\', \n+\t\t\thelp=\'Filter lower bound is a 0.00 percentages\')\n+\t\t\n+\t\tparser.add_option(\'-U\', \'--upper\', type=\'float\', dest=\'upper\',\n+\t\t\thelp=\'Filter upper bound is a 0.00 percentages\')\n+\n+\t\tparser.add_option(\'-o\', \'--output\', type=\'string\', dest=\'output\', \n+\t\t\thelp=\'Path of output file to create\')\n+\n+\t\tparser.add_option(\'-T\', \'--tree\', dest=\'tree\', default=False, action=\'store_true\', help=\'Generate Phylogenetic Tree output file\')\n+\n+\t\tparser.add_option(\'-v\', \'--version\', dest=\'version\', default=False, action=\'store_true\', help=\'Version number\')\n+\n+\t\t# Could also have -D INT decimal precision included for ffprwn .\n+\t\t\t\n+\t\toptions, args = parser.parse_args()\n+\n+\t\tif options.version:\n+\t\t\tprint VERSION_NUMBER\n+\t\t\treturn\n+\t\t\n+\t\timport time\n+\t\ttime_start = time.time()\n+\n+\t\ttry:\n+\t\t\tin_files = args[:]\n+\t\t\n+\t\texcept:\n+\t\t\tstop_err("Expecting at least 1 input data file.")\n+\n+\t\t\n+\t\t#ffptxt / ffpaa / ffpry\n+\t\tif options.type in \'text\':\n+\t\t\tcommand = \'ffptxt\'\n+\t\t\t\n+\t\telse:\n+\t\t\tif options.type == \'amino\':\n+\t\t\t\tcommand = \'ffpaa\'\n+\t\t\telse:\n+\t\t\t\tcommand = \'ffpry\'\n+\t\t\t\t\n+\t\t\tif options.disable:\n+\t\t\t\tcommand += \' -d\'\n+\t\t\t\t\n+\t\t\tif options.multiple:\n+\t\t\t\tcommand += \' -m\'\n+\t\t\n+\t\tcommand += \' -l \' + str(options.length)\n+\n+\t\tif len(in_files): #Note: app isn\'t really suited to stdio\n+\t\t\tcommand += \' "\' + \'" "\'.join(in_files) + \'"\'\n+\t\t\t\t\n+\t\t#ffpcol / ffpfilt\n+\t\tif options.filter != \'none\':\t\t\n+\t\t\tcommand += \' | ffpfilt\'\n+\t\t\tif options.filter != \'count\':\n+\t\t\t\tcommand += \' -\' + options.filter\n+\t\t\tif options.lower > 0:\n+\t\t\t\tcommand += \' --lower \' + str(options.lower)\n+\t\t\tif options.upper > 0:\n+\t\t\t\tcommand += \' --upper \' + str(options.upper)\n+\t\t\t\n+\t\telse:\n+\t\t\tcommand += \' | ffpcol\'\n+\n+\t\tif options.type in \'text\':\n+\t\t\tcommand += \' -t\'\n+\t\t\t\n+\t\telse:\n+\n+\t\t\tif options.type == \'amino\':\n+\t\t\t\tcommand += \' -a\'\n+\t\t\t\n+\t\t\tif options.disable:\n+\t\t\t\tcommand += \' -d\'\n+\t\t\t\n+\t\t#if options.normalize:\n+\t\tcommand += \' | ffprwn\'\n+\n+\t\t#Now create a taxonomy label file, ensuring a name exists for each profile.\n+\t\ttaxonomyNames = getTaxonomyNames(options.type, options.multiple, options.abbreviate, in_files, options.taxonomy)\n+\t\ttaxonomyTempFile = getTaxonomyFile(taxonomyNames)\n+\t\t# -p = Include phylip format \'infile\' of the taxon names to use. Very simple, just a list of fasta identifier names.\n+\t\tcommand += \' | ffpjsd -p \' + taxonomyTempFile\n+\n+\t\tif options.metric and len(options.metric) >0 :\n+\t\t\tcommand += \' --\' + options.metric\n+\t\t\tif options.similarity:\n+\t\t\t\tcommand += \' -s\'\n+\n+\t\t# Generate Newick (.nhx) formatted tree if we have at least 3 taxonomy items:\n+\t\tif options.tree:\n+\t\t\tif len(taxonomyNames) > 2:\n+\t\t\t\tcommand += \' | ffptree -q\' \n+\t\t\telse:\n+\t\t\t\tstop_err("For a phylogenetic tree display, one must have at least 3 ffp profiles.")\n+\n+\t\tresult = check_output(command)\n+\t\twith open(options.output,\'w\') as fw:\n+\t\t\tfw.writelines(result)\n+\t\tos.remove(taxonomyTempFile)\n+\n+if __name__ == \'__main__\':\n+\n+\ttime_start = time.time()\n+\n+\treportEngine = ReportEngine()\n+\treportEngine.__main__()\n+\t\n+\tprint(\'Execution time (seconds): \' + str(int(time.time()-time_start)))\n+\t\n' |
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| diff -r 000000000000 -r eb6e5e78a066 ffp_phylogeny.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ffp_phylogeny.xml Mon Feb 23 18:25:25 2015 -0500 |
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| b'@@ -0,0 +1,284 @@\n+<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.00">\n+\t<description>An alignment free comparison tool for phylogenetic analysis and text comparison</description>\n+\t<requirements>\n+\t\t<requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement>\n+\t</requirements>\n+\t\n+\t<macros>\n+\t\t<token name="@BINARY@">./ffp_phylogeny.py</token>\n+\t\t<import>ffp_macros.xml</import>\n+\t</macros>\n+\t<expand macro="requirements" />\n+ <command interpreter="python"><![CDATA[\n+\t\tffp_phylogeny.py\n+\t\t#for $i in $sequence.filesin\n+\t\t\t"$i" ## full file paths\n+\t\t#end for\n+\t\t-x "\n+\t\t#for $i in $sequence.filesin\n+\t\t\t$i.name, ## original file names\n+\t\t#end for\n+\t\t"\n+\t\t-t "$(sequence.file_type.split(\'-\')[0])"\n+\t\t-l "$length"\n+\t\t-o "$info"\n+\t\t##if $normalize:\n+\t\t##\t-n\n+\t\t##end if\n+\t\t#if $sequence.file_type != \'text\':\n+\t\t\t#if $sequence.file_type.find(\'multi\') > 0:\n+\t\t\t\t-m\n+\t\t\t#end if\n+\t\t\t#if $sequence.grouping:\n+\t\t\t\t-d\n+\t\t\t#end if\n+\t\t\t#if $metric:\n+\t\t\t\t-M "$metric"\n+\t\t\t#end if\n+\t\t\t#if $similarity:\n+\t\t\t\t-s\n+\t\t\t#end if\n+\t\t\t#if $abbreviate:\n+\t\t\t\t-a\n+\t\t\t#end if\t\t\t\n+\t\t#end if\n+\t\t#if $phylogeny.phylo_type == \'filter\':\n+\t\t\t-f "$phylogeny.filt.filter_type"\n+\t\t\t-L "$phylogeny.filt.lower"\n+\t\t\t-U "$phylogeny.filt.upper" \n+\t\t#end if\n+\t\t#if $tree:\n+\t\t\t-T\n+\t\t#end if\t\t\n+\n+\t\t##ffpjsd -n FLOAT , --normval=FLOAT\n+\t\t## For option -e, --euclid, change the n-norm distance (Default is n=2) to any other value where n > 1\n+\n+ ]]></command>\n+ <expand macro="stdio" />\n+ <inputs>\n+\n+\t\t<!-- Either amino acid or nucleotide input -->\n+\t\t<!-- Ideally we could determine from file content or suffix what type it is -->\n+\n+\t\t<param name="length" type="integer" min="1" max="25" label="l-mer length" value="6" help="String of valid characters of this length will be counted. Synonyms: feature, k-mer, n-gram, k-tuple" size="2"/>\n+\t\t<!--\n+\t\t<param name="normalize" label="Normalize counts into relative frequency" type="boolean" checked="true" help="" />\n+\t\t-->\n+\t\t<conditional name="sequence">\n+\t\t\t<param type="select" name="file_type" label="File type" help="Note: For phylogeny display, at least three profiles are required, as files or fasta sequences within a file.">\n+\t\t\t\t<option value="amino">Amino Acids, one sequence per file</option>\n+\t\t\t\t<option value="amino-multi">Amino Acids, multiple fasta sequences per file</option>\n+\t\t\t\t<option value="nucleotide">Nucleic acids, one sequence per file</option>\n+\t\t\t\t<option value="nucleotide-multi">Nucleic acids, multiple fasta sequences per file</option>\n+\t\t\t\t<option value="text">Text, single file</option>\n+\t\t\t</param>\n+\n+\t\t\t<when value="amino"><!-- ffpaa -->\n+\t\t\t\t<param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" />\n+\t\t\t\t<param name="grouping" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." />\n+\t\t\t</when>\n+\n+\t\t\t<when value="amino-multi">\n+\t\t\t\t<param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" />\n+\t\t\t\t<param name="grouping" label="Enable amino acid grouping" type="boolean" checked="true" help="Counts amino acids in groups rather than individually (usually advantageous, see below)." />\n+\t\t\t</when>\n+\t\t\t\t\t\t\n+\t\t\t<when value="nucleotide"><!-- ffpry -->\n+\t\t\t\t<param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" />\t\n+\t\t\t\t<param name="grouping" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) or pyrimidine(Y) rather than individually (usually advantageous)." />\n+\t\t\t</when>\n+\t\t\t\n+\t\t\t<when value="nucleotide-multi">\n+\t\t\t\t<param name="filesin" type="data" label="Select input file(s)" format="fasta" multiple="true" />\n+\t\t\t\t<param name="grouping" label="Enable purine / pyrimidine grouping" type="boolean" checked="true" help="Counts each nucleotide as a purine(R) o'..b'test>\n+\t\t<test>\n+\t\t\t<param name="length" value="2"/>\n+\t\t\t<param name="tree" value="0"/>\n+\t\t\t<param name="grouping" value="true"/>\n+\t\t\t<param name="file_type" value="nucleotide"/>\n+\t\t\t<param name="filesin" value="genome1,genome2"/>\n+\t\t\t<output name="info" file="test_length_2_output.tabular"/>\n+\t\t</test>\n+\t</tests>\n+\n+ <help><![CDATA[\n+ \n+.. class:: infomark\n+\n+\n+**What it does**\n+\n+FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.\n+\n+This galaxy tool prepares a mini-pipeline consisting of **[ffpry | ffpaa | ffptxt] > [ ffpfilt | ffpcol > ffprwn] > ffpjsd > ffptree** . The last step is optional - by deselecting the "Generate Tree Phylogeny" checkbox, the tool will output a distance matrix rather than a Newick (.nhx) formatted tree file.\n+\n+Each sequence or text file has a profile containing tallies of each feature found. A feature is a string of valid characters of given length. \n+\n+For nucleotide data, by default each character (ATGC) is grouped as either purine(R) or pyrmidine(Y) before being counted.\n+\n+For amino acid data, by default each character is grouped into one of the following:\n+(ST),(DE),(KQR),(IVLM),(FWY),C,G,A,N,H,P. Each group is represented by the first character in its series.\n+\n+One other key concept is that a given feature, e.g. "TAA" is counted in forward \n+AND reverse directions, mirroring the idea that a feature's orientation is not\n+so important to distinguish when it comes to alignment-free comparison. \n+The counts for "TAA" and "AAT" are merged.\n+ \n+The labeling of the resulting counted feature items is perhaps the trickiest\n+concept to master. Due to computational efficiency measures taken by the \n+developers, a feature that we see on paper as "TAC" may be stored and labeled \n+internally as "GTA", its reverse compliment. One must look for the alternative\n+if one does not find the original. \n+\n+Also note that in amino acid sequences the stop codon "*" (or any other character \n+that is not in the Amino acid alphabet) causes that character frame not to be\n+counted. Also, character frames never span across fasta entries.\n+\n+A few tutorials:\n+ * http://sourceforge.net/projects/ffp-phylogeny/files/Documentation/tutorial.pdf\n+ * https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny\n+\n+-------\n+\n+.. class:: warningmark\n+\n+**Note**\n+\n+Taxonomy label details: If each file contains one profile, the file\'s name is used to label the profile.\n+If each file contains fasta sequences to profile individually, their fasta identifiers will be used to label them.\n+The "short labels" option will find the shortest label that uniquely identifies each profile.\n+Either way, there are some quirks: ffpjsd clips labels to 10 characters if they are greater than 50 characters, so all labels are trimmed to 50 characters first.\n+Also "id" is prefixed to any numeric label since some tree visualizers won\'t show purely numeric labels.\n+In the accidental case where a Fasta sequence label is a duplicate of a previous one it will be prefixed by "DupLabel-".\n+\n+The command line ffpjsd can hang if one provides an l-mer length greater than the length of file content.\n+One must identify its process id (">ps aux | grep ffpjsd") and kill it (">kill [process id]").\n+-------\n+\n+**References**\n+\n+The original ffp-phylogeny code is at http://ffp-phylogeny.sourceforge.net/ .\n+This tool uses Aaron Petkau\'s modified version: https://github.com/apetkau/ffp-3.19-custom .\n+ \n+The development of the ff-phylogeny should be attributed to:\n+\n+Sims GE, Jun S-R, Wu GA, Kim S-H. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2677-2682. doi:10.1073/pnas.0813249106.\n+\n+ ]]></help>\n+</tool>\n+\n+\n' |
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| diff -r 000000000000 -r eb6e5e78a066 tarballit.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tarballit.sh Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,2 @@ +#!/bin/bash + tar -zcvf ffp_phylogeny.tar.gz * --exclude "*~" --exclude "tool_test_output*" --exclude "*gz" |
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| diff -r 000000000000 -r eb6e5e78a066 test-data/genome1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome1 Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,2 @@ +>genome1 +AATT |
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| diff -r 000000000000 -r eb6e5e78a066 test-data/genome2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome2 Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,2 @@ +>genome2 +AAGG |
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| diff -r 000000000000 -r eb6e5e78a066 test-data/test_length_1_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_length_1_output.tabular Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,3 @@ +2 +genome1 0.00e+00 1.89e-01 +genome2 1.89e-01 0.00e+00 |
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| diff -r 000000000000 -r eb6e5e78a066 test-data/test_length_2_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_length_2_output.tabular Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,3 @@ +2 +genome1 0.00e+00 4.58e-01 +genome2 4.58e-01 0.00e+00 |
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| diff -r 000000000000 -r eb6e5e78a066 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Feb 23 18:25:25 2015 -0500 |
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| @@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ffp-phylogeny" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone https://github.com/apetkau/ffp-3.19-custom.git ffp-phylogeny</action> + <action type="shell_command">git reset --hard d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3</action> + <action type="shell_command">./configure --disable-gui --prefix=$INSTALL_DIR</action> + <action type="make_install"></action> + <!-- action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action --> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + apetkau/ffp-3.19-custom is a customized version of http://sourceforge.net/projects/ffp-phylogeny/ + </readme> + </package> +</tool_dependency> + |