Ancestral Reconstruction Pipeline: Difference between revisions

Revision as of 21:22, 25 April 2014

-d<directory of input synmap files>
-g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
-w w1,w2,w3,w4 <list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?>
-s < subgenome_file>
-o <output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files>

-i <input file or directory>
- - File type is a set of vertex vertex weight
  - note: if directory, will batch process all files
-o <outfile or directory>

@@ Line 6: / Line 6: @@
 === Plan for refactoring ===
-# GetGenomes: remove config file, add option to specify output dir for output files
+==== GetGenomes: remove config file, add option to specify output dir for output files ====
-## -d&lt;directory of input synmap files&gt;
+* -d&lt;directory of input synmap files&gt;
-** -g gid1,gid2,gid3,gid4... &lt;list of common separated coge genome ids&gt;
+* -g gid1,gid2,gid3,gid4... &lt;list of common separated coge genome ids&gt;
-** -w w1,w2,w3,w4 &lt;list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?&gt;
+* -w w1,w2,w3,w4 &lt;list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?&gt;
-** -s < subgenome_file>
+* -s < subgenome_file>
-** -o &lt;output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files&gt;
+* -o &lt;output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files&gt;
-*MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for
+====MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for ====
-** -i &lt;input file or directory&gt;
+* -i &lt;input file or directory&gt;
 *** File type is a set of vertex vertex weight
 *** note: if directory, will batch process all files
-** -o &lt;outfile or directory&gt;
+* -o &lt;outfile or directory&gt;