Mercurial > repos > damion > ffp_phylogeny
changeset 3:79a4a86981d3 draft default tip
Uploaded
| author | damion |
|---|---|
| date | Thu, 23 Apr 2015 17:47:39 -0400 |
| parents | 671667722d3d |
| children | |
| files | README.md ffp_phylogeny.py ffp_phylogeny.xml test.txt |
| diffstat | 4 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/README.md Fri Mar 20 14:27:19 2015 -0400 +++ b/README.md Thu Apr 23 17:47:39 2015 -0400 @@ -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.
--- a/ffp_phylogeny.py Fri Mar 20 14:27:19 2015 -0400 +++ b/ffp_phylogeny.py Thu Apr 23 17:47:39 2015 -0400 @@ -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',
--- a/ffp_phylogeny.xml Fri Mar 20 14:27:19 2015 -0400 +++ b/ffp_phylogeny.xml Thu Apr 23 17:47:39 2015 -0400 @@ -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"