Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/mothur_wrapper.py @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 27 Jun 2011 10:12:25 -0500 |
| parents | e2e2071d2c62 |
| children | 370b3fc4e7d3 |
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| 6:ce6e81622c6a | 7:7bfe1f843858 |
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| 2 | 2 |
| 3 """ | 3 """ |
| 4 http://www.mothur.org/ | 4 http://www.mothur.org/ |
| 5 | 5 |
| 6 Supports mothur version | 6 Supports mothur version |
| 7 mothur v.1.17.0 | 7 mothur v.1.20.0 |
| 8 | 8 |
| 9 Class encapsulating Mothur galaxy tool. | 9 Class encapsulating Mothur galaxy tool. |
| 10 Expect each invocation to include: | 10 Expect each invocation to include: |
| 11 Here is an example call to this script with an explanation before each param : | 11 Here is an example call to this script with an explanation before each param : |
| 12 mothur_wrapper.py | 12 mothur_wrapper.py |
| 26 # specifies files to copy to the new_file_path | 26 # specifies files to copy to the new_file_path |
| 27 # The list is separated by commas | 27 # The list is separated by commas |
| 28 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) | 28 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) |
| 29 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output | 29 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output |
| 30 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' | 30 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' |
| 31 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree | 31 ## Before version 1.18.0 Many mothur commands first required data to be read into memory using: read.otu, read.dist, or read.tree |
| 32 # This prequisite command and its params are prefixed with 'READ_' | 32 # This prequisite command and its params are prefixed with 'READ_' |
| 33 --READ_cmd='read.otu' | 33 --READ_cmd='read.otu' |
| 34 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat | 34 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat |
| 35 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat' | 35 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat' |
| 36 --READ_label='unique,0.07' | 36 --READ_label='unique,0.07' |
| 174 For example - read.dist required a phylip or (column and name) argument. | 174 For example - read.dist required a phylip or (column and name) argument. |
| 175 The complexity of inputs should be handled by the glaxy tool xml file. | 175 The complexity of inputs should be handled by the glaxy tool xml file. |
| 176 """ | 176 """ |
| 177 cmd_dict = dict() | 177 cmd_dict = dict() |
| 178 cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) | 178 cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) |
| 179 #cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) | |
| 180 cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) | 179 cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) |
| 181 cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) | 180 cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) |
| 182 cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) | 181 cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) |
| 183 #cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']}) | |
| 184 cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']}) | 182 cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']}) |
| 185 #cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']}) | |
| 186 cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']}) | 183 cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']}) |
| 187 #catchall | 184 #catchall |
| 188 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) | 185 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) |
| 189 #cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']}) | |
| 190 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','processors']}) | 186 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','processors']}) |
| 191 #cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']}) | |
| 192 cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','processors']}) | 187 cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','processors']}) |
| 193 #cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) | |
| 194 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) | 188 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) |
| 195 #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']}) | |
| 196 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']}) | 189 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']}) |
| 197 #cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['keep','short']}) | 190 cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']}) |
| 198 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']}) | 191 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']}) |
| 199 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) | 192 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) |
| 200 #cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) | |
| 201 cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) | 193 cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) |
| 202 cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) | 194 cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) |
| 203 #cmd_dict['cluster'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']}) | |
| 204 cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']}) | 195 cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']}) |
| 205 #cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['method','cutoff','hard','precision']}) | |
| 206 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']}) | 196 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']}) |
| 207 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) | 197 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) |
| 208 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) | 198 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) |
| 209 #cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']}) | |
| 210 cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']}) | 199 cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']}) |
| 211 #cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']}) | |
| 212 cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']}) | 200 cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']}) |
| 213 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']}) | 201 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']}) |
| 214 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) | 202 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) |
| 203 cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups']}) | |
| 215 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) | 204 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) |
| 216 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) | 205 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []}) |
| 217 #cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','processors']}) | 206 cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []}) |
| 218 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']}) | 207 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']}) |
| 219 #cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']}) | 208 cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','processors']}) |
| 220 cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output']}) | |
| 221 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []}) | 209 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []}) |
| 222 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) | 210 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) |
| 223 #cmd_dict['get.group'] = dict({'required' : [], 'optional' : []}) | |
| 224 cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []}) | 211 cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []}) |
| 225 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) | 212 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) |
| 226 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) | 213 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) |
| 227 ##cmd_dict['get.otulist'] = dict({'required' : [], 'optional' : []}) | |
| 228 cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']}) | 214 cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']}) |
| 229 #cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']}) | |
| 230 cmd_dict['get.oturep'] = dict({'required' : ['fasta','list',['phylip','column']], 'optional' : ['name','label','group','groups','sorted','precision','cutoff','large','weighted']}) | 215 cmd_dict['get.oturep'] = dict({'required' : ['fasta','list',['phylip','column']], 'optional' : ['name','label','group','groups','sorted','precision','cutoff','large','weighted']}) |
| 231 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) | 216 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) |
| 232 ##cmd_dict['get.rabund'] = dict({'required' : [],'optional' : []}) | |
| 233 cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']}) | 217 cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']}) |
| 234 #cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']}) | |
| 235 cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']}) | 218 cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']}) |
| 236 ##cmd_dict['get.sabund'] = dict({'required' : [],'optional' : []}) | |
| 237 cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']}) | 219 cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']}) |
| 238 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) | 220 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) |
| 239 ##cmd_dict['get.sharedseqs'] = dict({'required' : [], 'optional' : []}) | |
| 240 cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']}) | 221 cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']}) |
| 241 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']}) | 222 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']}) |
| 242 #cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) | |
| 243 cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) | 223 cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) |
| 244 #cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']}) | |
| 245 cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']}) | 224 cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']}) |
| 246 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) | 225 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) |
| 247 cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']}) | 226 cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']}) |
| 248 #cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']}) | |
| 249 cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']}) | 227 cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']}) |
| 250 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) | 228 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) |
| 251 cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) | 229 cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) |
| 252 #cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : ['output']}) | |
| 253 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) | 230 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []}) |
| 254 cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups','ordergroup']}) | 231 cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups','ordergroup']}) |
| 255 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) | 232 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) |
| 256 cmd_dict['merge.files'] = dict({'required' : ['input','output']}) | 233 cmd_dict['merge.files'] = dict({'required' : ['input','output']}) |
| 257 cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']}) | 234 cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']}) |
| 258 #cmd_dict['metastats'] = dict({'required' : ['design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) | |
| 259 cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) | 235 cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) |
| 260 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) | 236 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) |
| 261 #cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']}) | |
| 262 cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']}) | 237 cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']}) |
| 263 ##cmd_dict['otu.hierarchy'] = dict({'required' : [], 'optional' : []}) | |
| 264 cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']}) | 238 cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']}) |
| 265 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) | 239 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) |
| 266 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) | 240 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) |
| 267 #cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']}) | |
| 268 cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']}) | 241 cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']}) |
| 269 #cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']}) | |
| 270 cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']}) | 242 cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']}) |
| 271 #cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []}) | |
| 272 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']}) | 243 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']}) |
| 273 #cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','scale','rarefy','collect','summary','processors']}) | 244 cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']}) |
| 274 cmd_dict['phylo.diversity'] = dict({'required' : ['tree','group'],'optional' : ['name','groups','iters','freq','scale','rarefy','collect','summary','processors']}) | |
| 275 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) | 245 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) |
| 276 #cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['names','diffs']}) | |
| 277 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs']}) | 246 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs']}) |
| 278 #cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']}) | |
| 279 cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']}) | 247 cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']}) |
| 280 #cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']}) | |
| 281 cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']}) | 248 cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']}) |
| 282 #cmd_dict['read.dist'] = dict({'required' : [['phylip','column']], 'optional' : ['name','cutoff','hard','precision','sim','group']}) | |
| 283 #cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']], 'optional' : ['label','group','groups','ordergroup']}) | |
| 284 #cmd_dict['read.tree'] = dict({'required' : ['tree'], 'optional' : ['name','group']}) | |
| 285 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) | 249 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) |
| 286 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) | 250 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) |
| 287 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) | 251 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) |
| 288 #cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) | |
| 289 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) | 252 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) |
| 290 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) | 253 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) |
| 291 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) | 254 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) |
| 292 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) | 255 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) |
| 293 cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']}) | 256 cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']}) |
| 294 cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) | 257 cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) |
| 295 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) | 258 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) |
| 296 #cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []}) | |
| 297 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']}) | 259 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']}) |
| 298 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) | 260 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) |
| 299 #cmd_dict['summary.seqs'] = dict({'required' : ['fasta'],'outputs' : ['names']}) | |
| 300 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']}) | 261 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']}) |
| 301 #cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']}) | |
| 302 cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']}) | 262 cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']}) |
| 303 #cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']}) | |
| 304 cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) | 263 cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) |
| 305 #cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']}) | |
| 306 cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']}) | 264 cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']}) |
| 307 cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) | 265 cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) |
| 308 #cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) | |
| 309 cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) | 266 cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) |
| 310 #cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) | |
| 311 cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) | 267 cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) |
| 312 #cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['names']}) | |
| 313 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']}) | 268 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']}) |
| 314 #cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) | |
| 315 cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) | 269 cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) |
| 316 ## | |
| 317 """ | |
| 318 cmd_dict['merge.files'] = dict({'required' : ['input','output']}) | |
| 319 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : ['output']}) | |
| 320 cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']}) | |
| 321 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], | |
| 322 'outputs' : ['.names']}) | |
| 323 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']}) | |
| 324 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']}) | |
| 325 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['names']}) | |
| 326 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','names'], 'optional' : []}) | |
| 327 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['keep','short']}) | |
| 328 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']}) | |
| 329 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']}) | |
| 330 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']}) | |
| 331 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]}) | |
| 332 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) | |
| 333 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']}) | |
| 334 cmd_dict['align.seqs'] = dict({'required' : ['candidate','template'], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','processors']}) | |
| 335 cmd_dict['align.check'] = dict({'required' : ['fasta','map']}) | |
| 336 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['names','diffs']}) | |
| 337 cmd_dict['bin.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','label','group']}) | |
| 338 cmd_dict['classify.seqs'] = dict({'required' : ['fasta','template','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','processors']}) | |
| 339 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']}) | |
| 340 # label=0.01-0.02-0.03 from 0.01,0.02,0.03 string.replace(options.label,',','-') | |
| 341 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']}) | |
| 342 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','template'], 'optional' : ['filter','mask','window','numwanted','processors']}) | |
| 343 cmd_dict['chimera.check'] = dict({'required' : ['fasta','template'], 'optional' : ['ksize','svg','name','increment','processors']}) | |
| 344 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','template'], 'optional' : ['conservation','quantile','filter','mask','window','increment','processors']}) | |
| 345 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']}) | |
| 346 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','processors']}) | |
| 347 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']}) | |
| 348 cmd_dict['read.dist'] = dict({'required' : [['phylip','column']], 'optional' : ['name','cutoff','hard','precision','sim','group']}) | |
| 349 cmd_dict['read.otu'] = dict({'required' : [['rabund','sabund','list','shared','relabund']], 'optional' : ['label','group','groups','ordergroup']}) | |
| 350 cmd_dict['read.tree'] = dict({'required' : ['tree'], 'optional' : ['name','group']}) | |
| 351 cmd_dict['cluster'] = dict({'required' : [] , 'optional' : ['method','cutoff','hard','precision']}) | |
| 352 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund']}) | |
| 353 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']}) | |
| 354 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']}) | |
| 355 cmd_dict['metastats'] = dict({'required' : ['design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']}) | |
| 356 cmd_dict['summary.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','groupmode']}) | |
| 357 cmd_dict['summary.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','all','distance']}) | |
| 358 cmd_dict['collect.single'] = dict({'required' : [], 'optional' : ['calc','abund','size','label','freq']}) | |
| 359 cmd_dict['collect.shared'] = dict({'required' : [], 'optional' : ['calc','label','freq','groups','all']}) | |
| 360 cmd_dict['rarefaction.single'] = dict({'required' : [], 'optional' : ['calc','abund','iters','label','freq','processors']}) | |
| 361 cmd_dict['rarefaction.shared'] = dict({'required' : [], 'optional' : ['label','iters','groups','jumble']}) | |
| 362 cmd_dict['normalize.shared'] = dict({'required' : [], 'optional' : ['label','method','norm','groups']}) | |
| 363 cmd_dict['dist.shared'] = dict({'required' : [], 'optional' : ['calc','label','groups','output']}) | |
| 364 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']}) | |
| 365 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : []}) | |
| 366 cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']}) | |
| 367 cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) | |
| 368 cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) | |
| 369 cmd_dict['parsimony'] = dict({'required' : [], 'optional' : ['groups','iters','random','processors']}) | |
| 370 cmd_dict['sffinfo'] = dict({'required' : ['sff'], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']}) | |
| 371 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []}) | |
| 372 cmd_dict['heatmap.bin'] = dict({'required' : [], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']}) | |
| 373 cmd_dict['heatmap.sim'] = dict({'required' : [], 'optional' : ['calc','phylip','column','name','label','groups']}) | |
| 374 cmd_dict['venn'] = dict({'required' : [], 'optional' : ['calc','label','groups','abund','nseqs','permute']}) | |
| 375 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : []}) | |
| 376 cmd_dict['pca'] = dict({'required' : [], 'optional' : ['label','groups','metric']}) | |
| 377 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']}) | |
| 378 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']}) | |
| 379 cmd_dict['get.group'] = dict({'required' : [], 'optional' : []}) | |
| 380 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']}) | |
| 381 cmd_dict['phylo.diversity'] = dict({'required' : [],'optional' : ['groups','iters','freq','scale','rarefy','collect','summary','processors']}) | |
| 382 cmd_dict['get.oturep'] = dict({'required' : ['fasta','list'], 'optional' : ['phylip','column','name','label','group','groups','sorted','precision','cutoff','large','weighted']}) | |
| 383 cmd_dict['get.relabund'] = dict({'required' : [],'optional' : ['scale','label','groups']}) | |
| 384 cmd_dict['libshuff'] = dict({'required' : [],'optional' : ['iters','form','step','cutoff']}) | |
| 385 # clearcut options not needed in galaxy: 'version','verbose','quiet','stdout' | |
| 386 cmd_dict['clearcut'] = dict({'required' : [['list','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']}) | |
| 387 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) | |
| 388 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']}) | |
| 389 cmd_dict['bootstrap.shared'] = dict({'required' : [], 'optional' : ['calc','groups','iters','label']}) | |
| 390 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['method','cutoff','hard','precision']}) | |
| 391 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) | |
| 392 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','taxonomy']}) | |
| 393 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) | |
| 394 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']}) | |
| 395 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']}) | |
| 396 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']}) | |
| 397 | |
| 398 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']}) | |
| 399 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label']}) | |
| 400 cmd_dict['indicator'] = dict({'required' : ['tree',['shared','relabund']], 'optional' : ['groups','label','design']}) | |
| 401 | |
| 402 cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) | |
| 403 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) | |
| 404 cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']}) | |
| 405 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']}) | |
| 406 cmd_dict['make,fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []}) | |
| 407 """ | |
| 408 | 270 |
| 409 parser = optparse.OptionParser() | 271 parser = optparse.OptionParser() |
| 410 # Options for managing galaxy interaction | 272 # Options for managing galaxy interaction |
| 411 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' ) | 273 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' ) |
| 412 parser.add_option( '--cmd', dest='cmd', help='The mothur command' ) | 274 parser.add_option( '--cmd', dest='cmd', help='The mothur command' ) |
| 487 parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' ) | 349 parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' ) |
| 488 parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' ) | 350 parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' ) |
| 489 parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' ) | 351 parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' ) |
| 490 parser.add_option( '--precision', dest='precision', type="int", help='' ) | 352 parser.add_option( '--precision', dest='precision', type="int", help='' ) |
| 491 parser.add_option( '--threshold', dest='threshold', type="float", help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' ) | 353 parser.add_option( '--threshold', dest='threshold', type="float", help='Cutoff at which an alignment is deemed bad and the reverse complement may be tried, 0.0 - 1.0 default 0.50' ) |
| 354 parser.add_option( '--sim', dest='sim', help='Calculate similarity rather than distance' ) | |
| 492 parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' ) | 355 parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' ) |
| 493 parser.add_option( '--label', dest='label', type='string', action="callback", callback=multi_val_callback, help='Distance levels you would like a output files created for(separated by commas or dashes)' ) | 356 parser.add_option( '--label', dest='label', type='string', action="callback", callback=multi_val_callback, help='Distance levels you would like a output files created for(separated by commas or dashes)' ) |
| 494 parser.add_option( '--filter', dest='filter', help='If true, a 50% soft filter will be applied' ) | 357 parser.add_option( '--filter', dest='filter', help='If true, a 50% soft filter will be applied' ) |
| 495 parser.add_option( '--correction', dest='correction', help='If true, square root of the distances is used instead of the distance value' ) | 358 parser.add_option( '--correction', dest='correction', help='If true, square root of the distances is used instead of the distance value' ) |
| 496 parser.add_option( '--window', dest='window', type="int", help='Window size for searching for chimeras, default is 1/4 sequence length' ) | 359 parser.add_option( '--window', dest='window', type="int", help='Window size for searching for chimeras, default is 1/4 sequence length' ) |
| 505 parser.add_option( '--trump', dest='trump', help='Remove a column if the trump character is found at that position in any sequence of the alignment.' ) | 368 parser.add_option( '--trump', dest='trump', help='Remove a column if the trump character is found at that position in any sequence of the alignment.' ) |
| 506 parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' ) | 369 parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' ) |
| 507 parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' ) | 370 parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' ) |
| 508 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' ) | 371 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' ) |
| 509 parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' ) | 372 parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' ) |
| 510 # parser.add_option( '--cutoff', dest='cutoff', type="float", help='Distance Cutoff threshold, discard larger distances' ) | |
| 511 parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' ) | 373 parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' ) |
| 512 parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' ) | 374 parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' ) |
| 513 parser.add_option( '--output', dest='output', help='Format for output' ) | 375 parser.add_option( '--output', dest='output', help='Format for output' ) |
| 514 parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' ) | 376 parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' ) |
| 515 parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' ) | 377 parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' ) |
| 582 parser.add_option( '--keepfirst', dest='keepfirst', help='trimming' ) | 444 parser.add_option( '--keepfirst', dest='keepfirst', help='trimming' ) |
| 583 parser.add_option( '--removelast', dest='removelast', help='trimming' ) | 445 parser.add_option( '--removelast', dest='removelast', help='trimming' ) |
| 584 parser.add_option( '--persample', dest='persample', help='sub sample option' ) | 446 parser.add_option( '--persample', dest='persample', help='sub sample option' ) |
| 585 parser.add_option( '--timing', dest='timing', help='timing option' ) | 447 parser.add_option( '--timing', dest='timing', help='timing option' ) |
| 586 parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' ) | 448 parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' ) |
| 449 parser.add_option( '--abskew', dest='abskew', type="float", help='Minimum abundance skew.') | |
| 450 parser.add_option( '--chimealns', dest='chimealns', help='Boolean - produce a file containing multiple alignments of query sequences') | |
| 451 parser.add_option( '--minh', dest='minh', type="float", help='mininum score to report chimera.') | |
| 452 parser.add_option( '--mindiv', dest='mindiv', type="float", help='mininum score to report chimera.') | |
| 453 parser.add_option( '--xn', dest='xn', type="float", help='weight of a no vote') | |
| 454 parser.add_option( '--dn', dest='dn', type="float", help='pseudo-count prior on number of no votes') | |
| 455 parser.add_option( '--xa', dest='xa', type="float", help='weight of an abstain vote') | |
| 456 parser.add_option( '--chunks', dest='chunks', type="int", help='the number of chunks to extract from the query sequence') | |
| 457 parser.add_option( '--minchunk', dest='minchunk', type="int", help='the minimum length of a chunk') | |
| 458 parser.add_option( '--idsmoothwindow', dest='idsmoothwindow', type="int", help='ength of id smoothing window') | |
| 459 parser.add_option( '--minsmoothid', dest='minsmoothid', type="float", help='minimum factional identity over smoothed window') | |
| 460 parser.add_option( '--maxp', dest='maxp', type="int", help='maximum number of candidate parents to consider') | |
| 461 parser.add_option( '--skipgaps', dest='skipgaps', help='Boolean') | |
| 462 parser.add_option( '--skipgaps2', dest='skipgaps2', help='Boolean') | |
| 463 parser.add_option( '--ucl', dest='ucl', help='') | |
| 464 parser.add_option( '--queryfract', dest='queryfract', type="float", help='') | |
| 465 parser.add_option( '--minlen', dest='minlen', type="int", help='Minimun sequence length' ) | |
| 466 parser.add_option( '--maxlen', dest='maxlen', type="int", help='Maximun sequence length' ) | |
| 587 # include read.otu options | 467 # include read.otu options |
| 588 parser.add_option( '--rabund', dest='rabund', help='' ) | 468 parser.add_option( '--rabund', dest='rabund', help='' ) |
| 589 parser.add_option( '--sabund', dest='sabund', help='' ) | 469 parser.add_option( '--sabund', dest='sabund', help='' ) |
| 590 parser.add_option( '--shared', dest='shared', help='' ) | 470 parser.add_option( '--shared', dest='shared', help='' ) |
| 591 parser.add_option( '--relabund', dest='relabund', help='' ) | 471 parser.add_option( '--relabund', dest='relabund', help='' ) |
| 740 if re.match('.*\.\.\.\s*$',line): | 620 if re.match('.*\.\.\.\s*$',line): |
| 741 continue | 621 continue |
| 742 if re.match('^\d*\s*$',line): | 622 if re.match('^\d*\s*$',line): |
| 743 continue | 623 continue |
| 744 # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands | 624 # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands |
| 745 if not options.cmd.startswith('unifrac') and re.match('^([0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info | 625 if not options.cmd.startswith('unifrac') and re.match('^(unique|[0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info |
| 746 continue | 626 continue |
| 747 if re.match('Output .*',line): | 627 if re.match('Output .*',line): |
| 748 break | 628 break |
| 749 if found_begin and info_chars < 200: | 629 if found_begin and info_chars < 200: |
| 750 info += "%s" % line | 630 info += "%s" % line |