| Previous changeset 2:671667722d3d (2015-03-20) |
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Commit message:
Uploaded |
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modified:
README.md ffp_phylogeny.py ffp_phylogeny.xml |
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removed:
test.txt |
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| diff -r 671667722d3d -r 79a4a86981d3 README.md --- a/README.md Fri Mar 20 14:27:19 2015 -0400 +++ b/README.md Thu Apr 23 17:47:39 2015 -0400 |
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| @@ -9,6 +9,8 @@ The original command line ffp-phylogeny code is at http://ffp-phylogeny.sourceforge.net/ . This tool uses Aaron Petkau's modified version: https://github.com/apetkau/ffp-3.19-custom . Aaron has quite a good writeup of the technique as well at https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny . +**Installation Note** : Your Galaxy server will need the groff package to be installed on it first (to generate ffp-phylogeny man pages). A cryptic error will occur if it isn't: "troff: fatal error: can't find macro file s". This is different from the "groff-base" package. + 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. 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. |
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| diff -r 671667722d3d -r 79a4a86981d3 ffp_phylogeny.py --- a/ffp_phylogeny.py Fri Mar 20 14:27:19 2015 -0400 +++ b/ffp_phylogeny.py Thu Apr 23 17:47:39 2015 -0400 |
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| @@ -245,7 +245,7 @@ help='Enables pearson correlation coefficient matrix and any of the binary distance measures to be turned into similarity matrixes.') parser.add_option('-f', '--filter', type='choice', dest='filter', default='none', - choices=['none','f','n','e','freq','norm','evd'], + choices=['none','count','f','n','e','freq','norm','evd'], help='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.') parser.add_option('-L', '--lower', type='float', dest='lower', |
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| diff -r 671667722d3d -r 79a4a86981d3 ffp_phylogeny.xml --- a/ffp_phylogeny.xml Fri Mar 20 14:27:19 2015 -0400 +++ b/ffp_phylogeny.xml Thu Apr 23 17:47:39 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.03"> +<tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.04"> <description>An alignment free comparison tool for phylogenetic analysis and text comparison</description> <requirements> <requirement type="package" version="0.3.19_d4382db015acec0e5cc43d6c1ac80ae12cb7e6b3">ffp-phylogeny</requirement> @@ -44,7 +44,7 @@ -a #end if #end if - #if $phylogeny.phylo_type == 'filter' + #if $phylogeny.phylo_type == 'filt' -f "$phylogeny.filt.filter_type" -L "$phylogeny.filt.lower" -U "$phylogeny.filt.upper" |
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| diff -r 671667722d3d -r 79a4a86981d3 test.txt --- a/test.txt Fri Mar 20 14:27:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -(2010EL_1798_v2_fa:8.45000000e-05,(2010EL_1786_v2_fa:7.20000000e-05, -2010EL_1796_v2_fa:1.25000000e-04):1.65000000e-05,2010EL_1749_v2_fa:1.11500000e-04); |