diff mothur/tools/mothur/mothur_wrapper.py @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/mothur_wrapper.py	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/mothur_wrapper.py	Tue Jun 07 17:39:06 2011 -0400
@@ -4,7 +4,7 @@
 http://www.mothur.org/
 
 Supports mothur version 
-mothur v.1.15.0
+mothur v.1.17.0
 
 Class encapsulating Mothur galaxy tool.
 Expect each invocation to include:
@@ -46,7 +46,7 @@
 
 debug = False
 #debug = True
-max_processors = 1
+max_processors = 2
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
@@ -54,6 +54,8 @@
 
 def __main__():
     # tranform the logfile into html 
+    # add extra file ouput
+    # add object tags for svg files
     def logfile_to_html(logfile_path,htmlfile_path,tmp_input_dir_name,tmp_output_dir_name,title="Mothur Logfile"):
         if debug:  print >> sys.stdout, 'logfile_to_html %s -> %s' % (logfile_path, htmlfile_path)
         if debug:  print >> sys.stdout, 'logfile_to_html input_dir:  %s' % tmp_input_dir_name
@@ -69,10 +71,18 @@
                     continue
 		elif line.find('put directory to ') >= 0:
                     continue
+		elif line.startswith('Mothur\'s directories:') :
+                    continue
+		elif line.startswith('outputDir=') :
+                    continue
 		elif line.startswith('Type ') :
                     continue
                 elif line.find(tmp_output_dir_name) >= 0:
-                    line = re.sub(out_pat,'<a href="\\1">\\1</a>',line)
+                    # if debug:  print >> sys.stdout, 'logfile_to_html #%s#' % line
+                    if line.strip().endswith('.svg'):
+                        line = re.sub(out_pat,' <object id="object" type="image/svg+xml" data="\\1">\\1</object> <br><a href="\\1">\\1</a> <hr/>',line)
+                    else:
+                        line = re.sub(out_pat,'<a href="\\1">\\1</a>',line)
                 elif line.find(tmp_input_dir_name) >= 0:
                     line = re.sub(in_pat,'\\1',line)
                 html.write(line)
@@ -165,6 +175,146 @@
     The complexity of inputs should be handled by the glaxy tool xml file.
     """
     cmd_dict = dict()
+    cmd_dict['align.check'] = dict({'required' : ['fasta','map']})
+   #cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']})
+    cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']})
+    cmd_dict['amova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['anosim'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+   #cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']})
+    cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']})
+   #cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']})
+    cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']})
+    #catchall
+    cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
+   #cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']})
+    cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','processors']})
+   #cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']})
+    cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','processors']})
+   #cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']})
+    cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']})
+   #cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','processors']})
+    cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','processors']})
+   #cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'],  'optional' : ['keep','short']})
+    cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'],  'optional' : ['countgaps','keep','short']})
+    cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']})
+   #cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']})
+    cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']})
+    cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']})
+   #cmd_dict['cluster'] = dict({'required' : [] ,  'optional' : ['method','cutoff','hard','precision']})
+    cmd_dict['cluster'] = dict({'required' : [['phylip','column']] ,  'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']})
+   #cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] ,  'optional' : ['method','cutoff','hard','precision']})
+    cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] ,  'optional' : ['name','method','cutoff','hard','sim','precision']})
+    cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] ,  'optional' : ['name','diffs','percent']})
+    cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] ,  'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']})
+   #cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']})
+    cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']})
+   #cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']})
+    cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']})
+    cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']})
+    cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
+    cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
+    cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'],  'optional' : []})
+   #cmd_dict['dist.seqs'] = dict({'required' : ['fasta'],  'optional' : ['calc','countends','output','cutoff','processors']})
+    cmd_dict['dist.seqs'] = dict({'required' : ['fasta'],  'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']})
+   #cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']})
+    cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output']})
+    cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []})
+    cmd_dict['filter.seqs'] = dict({'required' : ['fasta'],  'optional' : ['vertical','trump','soft','hard','processors']})
+   #cmd_dict['get.group'] = dict({'required' : [], 'optional' : []})
+    cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []})
+    cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']})
+    cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
+  ##cmd_dict['get.otulist'] = dict({'required' : [], 'optional' : []})
+    cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
+   #cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
+    cmd_dict['get.oturep'] = dict({'required' : ['fasta','list',['phylip','column']], 'optional' : ['name','label','group','groups','sorted','precision','cutoff','large','weighted']})
+    cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
+  ##cmd_dict['get.rabund'] = dict({'required' : [],'optional' : []})
+    cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
+   #cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']})
+    cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
+  ##cmd_dict['get.sabund'] = dict({'required' : [],'optional' : []})
+    cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']})
+    cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
+  ##cmd_dict['get.sharedseqs'] = dict({'required' : [], 'optional' : []})
+    cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
+    cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
+   #cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
+    cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
+   #cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']})
+    cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']})
+    cmd_dict['homova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']})
+   #cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']})
+    cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
+    cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
+    cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] ,  'optional' : []})
+   #cmd_dict['make.group'] = dict({'required' : ['fasta','groups'],  'optional' : ['output']})
+    cmd_dict['make.group'] = dict({'required' : ['fasta','groups'],  'optional' : []})
+    cmd_dict['make.shared'] = dict({'required' : ['list','group'],  'optional' : ['label','groups','ordergroup']})
+    cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] ,  'optional' : ['method','iters']})
+    cmd_dict['merge.files'] = dict({'required' : ['input','output']})
+    cmd_dict['merge.groups'] = dict({'required' : ['shared','design'],  'optional' : ['groups', 'label']})
+   #cmd_dict['metastats'] = dict({'required' : ['design'],  'optional' : ['groups', 'label','iters','threshold','sets','processors']})
+    cmd_dict['metastats'] = dict({'required' : ['shared','design'],  'optional' : ['groups', 'label','iters','threshold','sets','processors']})
+    cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
+   #cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']})
+    cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']})
+  ##cmd_dict['otu.hierarchy'] = dict({'required' : [], 'optional' : []})
+    cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']})
+    cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'],  'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
+    cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']})
+   #cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']})
+    cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']})
+   #cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']})
+    cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']})
+   #cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []})
+    cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
+   #cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','scale','rarefy','collect','summary','processors']})
+    cmd_dict['phylo.diversity'] = dict({'required' : ['tree','group'],'optional' : ['name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
+    cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
+   #cmd_dict['pre.cluster'] = dict({'required' : ['fasta'],  'optional' : ['names','diffs']})
+    cmd_dict['pre.cluster'] = dict({'required' : ['fasta'],  'optional' : ['name','diffs']})
+   #cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']})
+    cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']})
+   #cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']})
+    cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']})
+   #cmd_dict['read.dist'] = dict({'required' : [['phylip','column']],  'optional' : ['name','cutoff','hard','precision','sim','group']})
+   #cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']],  'optional' : ['label','group','groups','ordergroup']})
+   #cmd_dict['read.tree'] = dict({'required' : ['tree'],  'optional' : ['name','group']})
+    cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']})
+    cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
+    cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
+   #cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
+    cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
+    cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
+    cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
+    cmd_dict['screen.seqs'] = dict({'required' : ['fasta'],  'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']})
+    cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']})
+    cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
+    cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
+   #cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []})
+    cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']})
+    cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
+   #cmd_dict['summary.seqs'] = dict({'required' : ['fasta'],'outputs' : ['names']})
+    cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
+   #cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']})
+    cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
+   #cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']})
+    cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
+   #cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']})
+    cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']})
+    cmd_dict['trim.seqs'] = dict({'required' : ['fasta'],  'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']})
+   #cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
+    cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
+   #cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
+    cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
+   #cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['names']})
+    cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name']})
+   #cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','abund','nseqs','permute']})
+    cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute']})
+    ##
+    """
     cmd_dict['merge.files'] = dict({'required' : ['input','output']})
     cmd_dict['make.group'] = dict({'required' : ['fasta','groups'],  'optional' : ['output']})
     cmd_dict['merge.groups'] = dict({'required' : ['shared','design'],  'optional' : ['groups', 'label']})
@@ -192,7 +342,7 @@
     cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']})
     cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']})
     cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']})
-    cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','processors']})
+    cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','template'], 'optional' : ['name','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','processors']})
     cmd_dict['dist.seqs'] = dict({'required' : ['fasta'],  'optional' : ['calc','countends','output','cutoff','processors']})
     cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'],  'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
     cmd_dict['read.dist'] = dict({'required' : [['phylip','column']],  'optional' : ['name','cutoff','hard','precision','sim','group']})
@@ -203,7 +353,7 @@
     cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] ,  'optional' : ['name','diffs','percent']})
     cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] ,  'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']})
     cmd_dict['metastats'] = dict({'required' : ['design'],  'optional' : ['groups', 'label','iters','threshold','sets','processors']})
-    cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode','processors']})
+    cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']})
     cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']})
     cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']})
     cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']})
@@ -214,21 +364,21 @@
     cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
     cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []})
     cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']})
-    cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','processors']})
-    cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','processors']})
+    cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
+    cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']})
     cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']})
     cmd_dict['sffinfo'] = dict({'required' : ['sff'], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
     cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []})
     cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
     cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']})
-    cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','nseqs','permute']})
+    cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','abund','nseqs','permute']})
     cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []})
     cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']})
     cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
     cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
     cmd_dict['get.group'] = dict({'required' : [], 'optional' : []})
     cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
-    cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','processors','scale','rarefy','collect','summary','processors']})
+    cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','scale','rarefy','collect','summary','processors']})
     cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
     cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']})
     cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']})
@@ -237,10 +387,7 @@
     cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
     cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
     cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']})
-    """
-    Mothur 1.15
-    """
-    cmd_dict['cluster.classic'] = dict({'required' : [] ,  'optional' : ['method','cutoff','hard','precision']})
+    cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] ,  'optional' : ['method','cutoff','hard','precision']})
     cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']})
     cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']})
     cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
@@ -251,6 +398,14 @@
     cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
     cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']})
     cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']})
+
+    cmd_dict['amova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['homova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['anosim'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
+    cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] ,  'optional' : ['method','iters']})
+    cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] ,  'optional' : []})
+    """
+
     parser = optparse.OptionParser()
     # Options for managing galaxy interaction
     parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout'  )
@@ -318,6 +473,7 @@
     # parser.add_option( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' )
     parser.add_option( '--candidate', dest='candidate', help=' file ' )
     parser.add_option( '--template', dest='template', help=' file ' )
+    parser.add_option( '--reference', dest='reference', help=' file ' )
     parser.add_option( '--dups', dest='dups', help='if True also apply to the aliases from the names files' )
     parser.add_option( '--keep', dest='keep', help='Either front or back to specify the which end of the sequence to keep' )
     parser.add_option( '--search', dest='search', help='Method for finding the template sequence: kmer, blast, suffix' )
@@ -353,6 +509,7 @@
     parser.add_option( '--output', dest='output', help='Format for output' )
     parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' )
     parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' )
+    parser.add_option( '--split', dest='split', help='Chimera split parameter, whether to detect trimeras and quadmeras' )
     parser.add_option( '--abund', dest='abund', type='int', help='Threshold for rare to Abundant OTU classification' )
     parser.add_option( '--size', dest='size', type='int', help='Size - sample size' )
     parser.add_option( '--groupmode', dest='groupmode', help='Collate groups into one result table' )
@@ -373,12 +530,15 @@
     parser.add_option( '--percent', dest='percent', type='int', help='(0-100 percent)' )
     parser.add_option( '--divergence', dest='divergence', type='float', help='Divergence cutoff for chimera determination' )
     parser.add_option( '--sff', dest='sff',  help='Sff file' )
+    parser.add_option( '--svg', dest='svg',  help='SVG' )
     parser.add_option( '--sfftxt', dest='sfftxt',  help='Generate a sff.txt file' )
     parser.add_option( '--flow', dest='flow',  help='Generate a flowgram file' )
     parser.add_option( '--trim', dest='trim', help='Whether sequences and quality scores are trimmed to the clipQualLeft and clipQualRight values' )
     parser.add_option( '--input', dest='input', help='' )
     parser.add_option( '--phylip', dest='phylip', help='' )
+    parser.add_option( '--phylip2', dest='phylip2', help='' )
     parser.add_option( '--column', dest='column', help='' )
+    parser.add_option( '--sort', dest='sort', help='specify sort order' )
     parser.add_option( '--sorted', dest='sorted', help='Input is presorted' )
     parser.add_option( '--showabund', dest='showabund', help='' )
     parser.add_option( '--short', dest='short', help='Keep sequences that are too short to chop' )
@@ -387,6 +547,7 @@
     parser.add_option( '--numotu', dest='numotu', help='' )
     parser.add_option( '--fontsize', dest='fontsize', help='' )
     parser.add_option( '--neqs', dest='neqs', help='' )
+    parser.add_option( '--random', dest='random', help='' )
     parser.add_option( '--permute', dest='permute', help='' )
     parser.add_option( '--rarefy', dest='rarefy', help='' )
     parser.add_option( '--collect', dest='collect', help='' )
@@ -408,6 +569,8 @@
     parser.add_option( '--sets', dest='sets', help='' )
     parser.add_option( '--metric', dest='metric', help='' )
     parser.add_option( '--epsilon', dest='epsilon', help='' )
+    parser.add_option( '--alpha', dest='alpha', help='' )
+    parser.add_option( '--root', dest='root', help='' )
     parser.add_option( '--axes', dest='axes', help='table of name column followed by columns of axis values' )
     parser.add_option( '--numaxes', dest='numaxes', help='the number of axes' )
     parser.add_option( '--metadata', dest='metadata', help='data table with columns of floating-point values' )
@@ -446,7 +609,14 @@
             os.makedirs(options.tmpdir)
         tmp_dir = options.tmpdir
     else:
-        tmp_dir = tempfile.mkdtemp()
+        if options.outputdir != None:
+            if not os.path.isdir(options.outputdir):
+                os.makedirs(options.outputdir)
+            tmp_dir = os.path.join(options.outputdir,'tmp') 
+            if not os.path.isdir(tmp_dir):
+                os.makedirs(tmp_dir)
+        else:
+            tmp_dir = tempfile.mkdtemp()
     if options.inputdir != None:
         if not os.path.isdir(options.inputdir):
             os.makedirs(options.inputdir)
@@ -478,11 +648,12 @@
     # print >> sys.stderr, cmd_opts
     # print >> sys.stderr, params # so will appear as blurb for file
     params.append('%s(%s)' % (options.cmd,cmd_opts))
+    if debug: params.append('get.current()')
     try:
         # Generate the mothur commandline 
         # http://www.mothur.org/wiki/Command_line_mode
         cmdline = 'mothur "#'  + '; '.join(params) + '"'
-        # print >> sys.stdout, '%s' % cmdline
+        if debug: print >> sys.stdout, '%s' % cmdline
         if tmp_dir == None or not os.path.isdir(tmp_dir):
             tmp_dir = tempfile.mkdtemp()
         tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
@@ -492,6 +663,7 @@
         proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
         # proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE )
         returncode = proc.wait()
+        if debug: print >> sys.stdout, 'returncode %d' % returncode
         tmp_stderr.close()
         # get stderr, allowing for case where it's very large
         tmp_stderr = open( tmp_stderr_name, 'rb' )
@@ -505,12 +677,26 @@
         except OverflowError:
             pass
         tmp_stderr.close()
+        tmp_stdout.close()
+        if debug: print >> sys.stdout, 'parse %s' % tmp_stdout_name
         if returncode != 0:
+            try:
+                # try to copy stdout to the logfile
+                for output in options.result.split(','):
+                    # Each item has a regex pattern and a file path to a galaxy dataset
+                    (pattern,path) = output.split(':')
+                    if debug: print >> sys.stdout, '%s -> %s' % (pattern,path)
+                    if pattern.find('\.logfile') > 0: 
+                        if path != None and os.path.exists(path):
+                            logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd)
+                        break
+            except:
+                pass
             raise Exception, stderr
         stdout = ''
         # Parse stdout to provide info
-        tmp_stdout.close()
         tmp_stdout = open( tmp_stdout_name, 'rb' )
+        # try to find a "little" something interesting to print as info for the galaxy interface
         info = ''
         if options.cmd.startswith('chimera') and not options.cmd.endswith('check'):
             pattern = '^.*$'
@@ -533,19 +719,32 @@
             info += "Chimeras: %d" % chimera_count
         else:
             found_begin = False
+            info_chars = 0
             for line in tmp_stdout:
                 if line.find(outputdir) >= 0:
                     continue
+	        if line.startswith('**************'):
+                    continue
                 if re.match('^Processing.*',line):
                     continue
+                if re.match('^Reading .*',line):
+                    continue
+                if re.match('^Merging .*',line):
+                    continue
+                if re.match('^DONE.*',line):
+                    continue
                 if re.match('.*\.\.\.\s*$',line):
                     continue
                 if re.match('^\d*\s*$',line):
                     continue
+                # if re.match('^(unique|[0-9.]*)(\t\d+)+',line):  # abundance from cluster commands 
+                if not options.cmd.startswith('unifrac') and re.match('^([0-9.]+)(\t\d+)*',line):  # abundance from cluster commands, allow unique line into info
+                    continue
                 if re.match('Output .*',line):
                     break
-                if found_begin:
+                if found_begin and info_chars < 200:
                     info += "%s" % line
+                    info_chars += len(line)
                 if re.match('mothur > ' + options.cmd + '\(.*\)', line):
                     found_begin = True
         tmp_stdout.close()
@@ -553,6 +752,15 @@
         # Collect output files
         flist = os.listdir(outputdir)
         if debug: print >> sys.stdout, '%s' % flist
+        # chimera.check can generate svg files, but they are not listed in the mothur.*.logfile, so we'll added them in here
+        if options.cmd == 'chimera.check':
+            svgs = []
+            mothurlog = None
+            for fname in flist:
+                if fname.endswith('.svg'):
+                    svgs.append(fname)
+                elif fname.endswith('.logfile'):
+                    mothurlog = fname
         # process option result first  
         # These are the known galaxy datasets listed in the --result= param
         if len(flist) > 0 and options.result:
@@ -573,23 +781,31 @@
                         if fname.endswith('.logfile'):  
                             # Make the logfile into html
                             logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd)
-                        elif False and outputdir == options.outputdir:
-                            # Use a hard link if outputdir is the extra_files_path
+                        elif outputdir == options.outputdir:
+                            # Use a hard link if outputdir is the extra_files_path, allows link from mothur logfile without copying data.
                             try:
+                                if debug: print >> sys.stdout, 'link %s  %s' % (fpath, path)
                                 os.link(fpath, path)
                             except:
+                                if debug: print >> sys.stdout, 'copy %s  %s' % (fpath, path)
                                 shutil.copy2(fpath, path)
                         else:
+                            if debug: print >> sys.stdout, 'copy2 %s  %s' % (fpath, path)
                             shutil.copy2(fpath, path)
                         break
+                # mothur.*.logfile may be in tmp_dir
                 # chimera.pintail e.g.  generates files in the working dir that we might want to save
                 if not found:
                     for fname in os.listdir(tmp_dir):
                         if debug: print >> sys.stdout, 'tmpdir %s match: %s' % (fname,re.match(pattern,fname))
                         if re.match(pattern,fname):
                             fpath = os.path.join(tmp_dir,fname)
-                            shutil.copy2(fpath, path)
-                            break
+                            if fname.endswith('.logfile'):
+                                # Make the logfile into html
+                                logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd)
+                            else:
+                                shutil.copy2(fpath, path)
+                                break
         # Handle the dynamically generated galaxy datasets
         # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
         # --new_datasets=   specifies files to copy to the new_file_path
@@ -605,7 +821,8 @@
                     if m:
                         fpath = os.path.join(outputdir,fname)
                         if len(m.groups()) > 0:
-                            root = m.groups()[0]
+                            # remove underscores since galaxy uses that as a field separator for dynamic datasets
+                            root = m.groups()[0].replace('_','')
                         else:
                             # remove  the ext from the name if it exists, galaxy will add back later
                             # remove underscores since galaxy uses that as a field separator for dynamic datasets
@@ -632,13 +849,18 @@
         try: 
             if outputdir != options.outputdir and os.path.exists(outputdir):
                 if os.path.islink(outputdir):
+                    if debug:  print >> sys.stdout, 'rm outputdir %s' % outputdir
                     os.remove(outputdir)
+                    if debug:  print >> sys.stdout, 'rmtree outputdir %s' % outputdir
                     shutil.rmtree(os.path.dirname(outputdir))
                 else:
+                    if debug:  print >> sys.stdout, 'rmtree %s' % outputdir
                     shutil.rmtree(outputdir)
             if inputdir != options.inputdir and os.path.exists(inputdir):
+                if debug:  print >> sys.stdout, 'rmtree %s' % inputdir
                 shutil.rmtree(inputdir)
         except:
+            if debug:  print >> sys.stdout, 'rmtree failed'  
             pass