Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/mothur_wrapper.py @ 13:4f797d3eee3a

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Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
author Jim Johnson <jj@umn.edu>
date Wed, 05 Oct 2011 10:34:44 -0500
parents 370b3fc4e7d3
children a6189f58fedb
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1 #!/usr/bin/env python
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2
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3 """
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4 http://www.mothur.org/
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5
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6 Supports mothur version
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7 mothur v.1.20.0
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8
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9 Class encapsulating Mothur galaxy tool.
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10 Expect each invocation to include:
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11 Here is an example call to this script with an explanation before each param :
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12 mothur_wrapper.py
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13 # name of a mothur command, this is required
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14 --cmd='summary.shared'
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15 # Galaxy output dataset list, these are output files that can be determined before the command is run
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16 # The items in the list are separated by commas
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17 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
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18 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
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19 # Galaxy output dataset extra_files_path direcotry in which to put all output files
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20 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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21 # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation
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22 # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
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23 --datasetid='2578'
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24 # The galaxy directory in which to copy all output files for dynamic dataset generation
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25 --new_file_path='/home/galaxy/data/database/tmp'
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26 # specifies files to copy to the new_file_path
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27 # The list is separated by commas
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28 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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29 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
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30 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
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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
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32 # This prequisite command and its params are prefixed with 'READ_'
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33 --READ_cmd='read.otu'
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34 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
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35 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
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36 --READ_label='unique,0.07'
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37 """
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38 # import pkg_resources;
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39 import logging, os, string, sys, tempfile, glob, shutil, types, urllib, optparse, re
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40 import shlex, subprocess
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41 from stat import *
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42
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43 log = logging.getLogger( __name__ )
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44
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45 assert sys.version_info[:2] >= ( 2, 4 )
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46
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47 debug = False
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48 #debug = True
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49 max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8
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50
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51 def stop_err( msg ):
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52 sys.stderr.write( "%s\n" % msg )
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53 sys.exit()
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54
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55 def __main__():
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56 # tranform the logfile into html
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57 # add extra file ouput
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58 # add object tags for svg files
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59 def logfile_to_html(logfile_path,htmlfile_path,tmp_input_dir_name,tmp_output_dir_name,title="Mothur Logfile"):
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60 if debug: print >> sys.stdout, 'logfile_to_html %s -> %s' % (logfile_path, htmlfile_path)
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61 if debug: print >> sys.stdout, 'logfile_to_html input_dir: %s' % tmp_input_dir_name
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62 if debug: print >> sys.stdout, 'logfile_to_html output_dir: %s' % tmp_output_dir_name
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63 txt = open(logfile_path,'r')
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64 in_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_input_dir_name) + '/(.+)'
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65 out_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_output_dir_name) + '/(.+)'
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66 html = open(htmlfile_path,'w')
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67 html.write("<html><head><title>%s</title></head>\n<body>\n<pre>\n" % title)
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68 try:
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69 for line in txt:
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70 if line.find('set.dir') >= 0:
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71 continue
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72 elif line.find('put directory to ') >= 0:
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73 continue
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74 elif line.startswith('Mothur\'s directories:') :
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75 continue
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76 elif line.startswith('outputDir=') :
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77 continue
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78 elif line.startswith('Type ') :
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79 continue
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80 elif line.find(tmp_output_dir_name) >= 0:
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81 # if debug: print >> sys.stdout, 'logfile_to_html #%s#' % line
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82 if line.strip().endswith('.svg'):
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83 line = re.sub(out_pat,' <object id="object" type="image/svg+xml" data="\\1">\\1</object> <br><a href="\\1">\\1</a> <hr/>',line)
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84 else:
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85 line = re.sub(out_pat,'<a href="\\1">\\1</a>',line)
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86 elif line.find(tmp_input_dir_name) >= 0:
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87 line = re.sub(in_pat,'\\1',line)
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88 html.write(line)
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89 except Exception, e:
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90 print(str(e))
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91 pass
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92 html.write('</pre>\n</body>\n</html>\n')
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93 html.close()
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94 #Overide the processors option
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95 def processors_callback(option, opt, value, parser):
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96 val = value if value <= max_processors else max_processors
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97 setattr(parser.values, option.dest, val)
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98 #Strip out "(xx)" confidence values from a taxonomy list
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99 def remove_confidence_callback(option, opt, value, parser):
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100 # val = "'" + re.sub('\(\d+\)','',value) + "'"
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101 setattr(parser.values, option.dest, re.sub('\(\d+\)','',value))
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102 #Mothur separates items in a list of values with hyphens
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103 def multi_val_callback(option, opt, value, parser):
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104 setattr(parser.values, option.dest, '-'.join(value.split(',')))
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105 #Handle list arguments that may contain dataset files
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106 def prepare_input(value,input_dir):
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107 """
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108 Mothur requires items in a list of input values to be separated by hyphens
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109 Change list separator from comma to hyphen
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110 If those items are files, copy them to the input dir.
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111 """
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112 if input_dir != None and value != None and isinstance(value, str):
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113 vals = []
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114 for val in value.split(','):
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115 if val[0] == '/' and os.path.isfile(val):
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116 (dir,fname) = os.path.split(val)
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117 try:
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118 os.symlink(val,os.path.join(input_dir,fname))
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119 except:
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120 shutil.copy(val,os.path.join(input_dir,fname))
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121 vals.append(fname)
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122 if debug: print >> sys.stderr, "scp %s %s" % (val, os.path.join(input_dir,fname))
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123 else:
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124 vals.append(val)
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125 return '-'.join(vals)
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126 return value
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127 #Parse Command Line and get a list of params
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128 # Prefix is used to differentiate between prerequisite commands: read.otu, read.dist, read.tree
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129 def get_params(cmd, options, input_dir, prefix=''):
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130 if debug: print >> sys.stderr, options
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131 params = []
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132 for opt in cmd_dict[cmd]['required']:
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133 if debug: print >> sys.stderr, opt
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134 if isinstance(opt,list): # One of these must be present
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135 missing = True
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136 for sel in opt:
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137 # if debug: print >> sys.stderr, sel
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138 try:
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139 value = prepare_input(getattr(options,prefix+sel), input_dir)
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140 if value != None:
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141 params.append('%s=%s' % (sel,value))
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142 missing = False
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143 except Exception, e:
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144 stop_err('Illegal option for cmd %s : %s %s' % (cmd,sel,e))
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145 if missing:
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146 stop_err('Missing a required parameter for %s, need one of %s' % (cmd,opt))
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147 else: # This option is required
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148 try:
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149 value = prepare_input(getattr(options,prefix+opt), input_dir)
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150 # if debug: print >> sys.stderr, value
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151 if value != None:
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152 params.append('%s=%s' % (opt,value))
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153 else:
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154 stop_err('Missing a required parameter for %s : %s' % (cmd,opt))
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155 except Exception, e:
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156 stop_err('Illegal option %s %s' % (opt,e))
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157 if 'optional' in cmd_dict[cmd]:
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158 for opt in cmd_dict[cmd]['optional']:
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159 # if debug: print >> sys.stderr, opt
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160 try:
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161 value = prepare_input(getattr(options,prefix+opt), input_dir)
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162 # if debug: print >> sys.stderr, value
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163 if value != None:
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164 params.append('%s=%s' % (opt,value))
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165 except Exception, e:
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166 # should distinguish between READ_ opts and cmd opts
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167 # stop_err('Illegal option for %s : %s' % (cmd,opt))
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168 pass
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169 return params
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170 """
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171 The command dict has a dict for each mothur command with required and options arguments
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172 The top level list of required arguments is interpreted that each value item is required and any list item represents a choice of arguments
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173 This covers many, but not all of the argument dependency requirements.
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174 For example - read.dist required a phylip or (column and name) argument.
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175 The complexity of inputs should be handled by the glaxy tool xml file.
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176 """
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177 cmd_dict = dict()
2
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178 cmd_dict['align.check'] = dict({'required' : ['fasta','map']})
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179 cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','save','processors']})
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180 cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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181 cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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182 cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']})
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183 cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']})
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184 #catchall
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185 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
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186 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']})
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187 cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']})
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188 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']})
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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','blastlocation','save','processors']})
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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']})
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191 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']})
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192 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']})
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193 cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors']})
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194 #clear.memory ## not needed in galaxy framework
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195 cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']})
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196 cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']})
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197 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']})
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198 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']})
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199 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']})
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200 cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']})
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201 cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']})
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202 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']})
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203 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
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204 cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups']})
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205 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
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206 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []})
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207 cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []})
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208 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']})
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209 cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','processors']})
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210 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []})
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211 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']})
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212 cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []})
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213 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']})
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214 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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215 cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
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216 cmd_dict['get.oturep'] = dict({'required' : ['fasta','list',['phylip','column']], 'optional' : ['name','label','group','groups','sorted','precision','cutoff','large','weighted']})
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217 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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218 cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
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219 cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
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220 cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']})
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221 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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222 cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
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223 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
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224 cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
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225 cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']})
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226 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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227 cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
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228 cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
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229 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
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230 cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []})
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231 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []})
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232 cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups','ordergroup']})
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233 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']})
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234 cmd_dict['merge.files'] = dict({'required' : ['input','output']})
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235 cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']})
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236 cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']})
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237 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
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238 cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']})
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239 cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']})
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240 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
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241 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']})
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parents: 1
diff changeset
242 cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']})
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jjohnson
parents: 1
diff changeset
243 cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']})
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jjohnson
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diff changeset
244 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
245 cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
2
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jjohnson
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diff changeset
246 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
247 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs']})
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diff changeset
248 cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']})
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diff changeset
249 cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']})
12
370b3fc4e7d3 Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
250 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']})
2
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jjohnson
parents: 1
diff changeset
251 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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jjohnson
parents: 1
diff changeset
252 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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parents: 1
diff changeset
253 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
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parents: 1
diff changeset
254 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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jjohnson
parents: 1
diff changeset
255 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
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parents: 1
diff changeset
256 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']})
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parents: 1
diff changeset
257 cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']})
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parents: 1
diff changeset
258 cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
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parents: 1
diff changeset
259 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
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jjohnson
parents: 1
diff changeset
260 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']})
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jjohnson
parents: 1
diff changeset
261 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
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parents: 1
diff changeset
262 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
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parents: 1
diff changeset
263 cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
264 cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
265 cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']})
13
4f797d3eee3a Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
Jim Johnson <jj@umn.edu>
parents: 12
diff changeset
266 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','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
267 cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
diff changeset
268 cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
269 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
270 cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
271
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
272 parser = optparse.OptionParser()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
273 # Options for managing galaxy interaction
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diff changeset
274 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
275 parser.add_option( '--cmd', dest='cmd', help='The mothur command' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
276 parser.add_option( '--inputdir', dest='inputdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
277 parser.add_option( '--outputdir', dest='outputdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
278 parser.add_option( '--tmpdir', dest='tmpdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
279 parser.add_option( '--tempdefault', dest='tempdefault', help='The default directory in which to search for input' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
280 parser.add_option( '--result', dest='result', help='The name pattern and destination for each output file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
281 parser.add_option( '--new_file_path', dest='new_file_path', help='The Galaxy new_file_path, dir for extra output datasets' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
282 parser.add_option( '--datasetid', dest='datasetid', help='The Galaxy new_file_path, dir for extra output datasets' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
283 parser.add_option( '--new_datasets', dest='new_datasets', help='The name pattern and datatype ext for ouputs' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
284 # Options for prerequisite Read commands
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
285 parser.add_option( '--READ_cmd', dest='READ_cmd', help='The mothur command' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
286 # required arguments for Read.dist
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
287 parser.add_option( '--READ_phylip', dest='READ_phylip', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
288 parser.add_option( '--READ_column', dest='READ_column', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
289 # required arguments for Read.otu
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
290 parser.add_option( '--READ_rabund', dest='READ_rabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
291 parser.add_option( '--READ_sabund', dest='READ_sabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
292 parser.add_option( '--READ_list', dest='READ_list', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
293 parser.add_option( '--READ_shared', dest='READ_shared', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
294 parser.add_option( '--READ_relabund', dest='READ_relabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
295 # required arguments for Read.tree
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
296 parser.add_option( '--READ_tree', dest='READ_tree', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
297 # optional arguments for Read cmds
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jjohnson
parents:
diff changeset
298 parser.add_option( '--READ_name', dest='READ_name', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
299 parser.add_option( '--READ_cutoff', dest='READ_cutoff', type="float", help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
300 parser.add_option( '--READ_hard', dest='READ_hard', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
301 parser.add_option( '--READ_precision', dest='READ_precision', type="int", help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
302 parser.add_option( '--READ_sim', dest='READ_sim', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
303 parser.add_option( '--READ_group', dest='READ_group', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
304 parser.add_option( '--READ_groups', dest='READ_groups', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
305 parser.add_option( '--READ_ordergroup', dest='READ_ordergroup', help='')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
306 parser.add_option( '--READ_label', dest='READ_label', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
307 # Parameter specified in mothur
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
308 parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
309 parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
310 parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
311 parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
312 parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
313 parser.add_option( '--qthreshold', dest='qthreshold', type="int", help='If at any point a base call in a sequence has a quality score below the value provided to the option, the sequence is terminated' )
5
e2e2071d2c62 Add missing qual params to trim.seqs
jj@dbw-galaxy-dev.msi.umn.edu
parents: 2
diff changeset
314 parser.add_option( '--qwindowaverage', dest='qwindowaverage', type="int", help='Remove sequences that have a window average quality below the value' )
e2e2071d2c62 Add missing qual params to trim.seqs
jj@dbw-galaxy-dev.msi.umn.edu
parents: 2
diff changeset
315 parser.add_option( '--qwindowsize', dest='qwindowsize', type="int", help='WIndow size for qwindowaverage' )
e2e2071d2c62 Add missing qual params to trim.seqs
jj@dbw-galaxy-dev.msi.umn.edu
parents: 2
diff changeset
316 parser.add_option( '--rollaverage', dest='rollaverage', type="int", help='Remove sequences that have a average quality below the value in a rolling window' )
e2e2071d2c62 Add missing qual params to trim.seqs
jj@dbw-galaxy-dev.msi.umn.edu
parents: 2
diff changeset
317 parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
318 parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
319 parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
320 parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
321 parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
322 parser.add_option( '--minlength', dest='minlength', type="int", help='Minimun sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
323 parser.add_option( '--maxlength', dest='maxlength', type="int", help='Maximun sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
324 parser.add_option( '--oligos', dest='oligos', help='The oligos option takes a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier.' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
325 parser.add_option( '--bdiffs', dest='bdiffs', type="int", help='Number of barcode differences to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
326 parser.add_option( '--pdiffs', dest='pdiffs', type="int", help='Number of primer differences to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
327 parser.add_option( '--tdiffs', dest='tdiffs', type="int", help='Total number of barcode and primer differences to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
328 parser.add_option( '--diffs', dest='diffs', type="int", help='Number of mismatched bases to allow between sequences in a group' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
329 parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
330 parser.add_option( '--name', dest='name', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
331 parser.add_option( '--accnos', dest='accnos', help='A file containing a list of names' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
332 parser.add_option( '--groups', dest='groups', help='pairwise group labels' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
333 parser.add_option( '--group', dest='group', help='A file containing a list of names' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
334 parser.add_option( '--list', dest='list', help='A file containing a list of names' )
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jjohnson
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diff changeset
335 parser.add_option( '--alignreport', dest='alignreport', help='A align.report file ' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
336 parser.add_option( '--taxonomy', dest='taxonomy', help='A Taxonomy file' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
337 parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
338 parser.add_option( '--taxon', dest='taxon', help='A Taxon' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
339 parser.add_option( '--taxlevel', dest='taxlevel', type="int", help='A Taxonomy level' )
0
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jjohnson
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diff changeset
340 # parser.add_option( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' )
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diff changeset
341 parser.add_option( '--candidate', dest='candidate', help=' file ' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
342 parser.add_option( '--template', dest='template', help=' file ' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
343 parser.add_option( '--reference', dest='reference', help=' file ' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff changeset
344 parser.add_option( '--dups', dest='dups', help='if True also apply to the aliases from the names files' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
345 parser.add_option( '--keep', dest='keep', help='Either front or back to specify the which end of the sequence to keep' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
346 parser.add_option( '--search', dest='search', help='Method for finding the template sequence: kmer, blast, suffix' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
347 parser.add_option( '--ksize', dest='ksize', type="int", help='Size of kmers (5 - 12)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
348 parser.add_option( '--align', dest='align', help='Alignment method: needleman, blastn, gotoh' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
349 parser.add_option( '--match', dest='match', type="float", help='Reward for a match, default is +1.0' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
350 parser.add_option( '--mismatch', dest='mismatch', type="float", help='Penalty for a mismatch, default is -1.0' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
351 parser.add_option( '--gapopen', dest='gapopen', type="float", help='Penalty for a opening, default is -2.0' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
352 parser.add_option( '--gapextend', dest='gapextend', type="float", help='Penalty for extending a gap, default is -1.0' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
353 parser.add_option( '--precision', dest='precision', type="int", help='' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
354 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' )
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
355 parser.add_option( '--sim', dest='sim', help='Calculate similarity rather than distance' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
356 parser.add_option( '--map', dest='map', help='File containing the secondary structure map.' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
357 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)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
358 parser.add_option( '--filter', dest='filter', help='If true, a 50% soft filter will be applied' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
359 parser.add_option( '--correction', dest='correction', help='If true, square root of the distances is used instead of the distance value' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
360 parser.add_option( '--window', dest='window', type="int", help='Window size for searching for chimeras, default is 1/4 sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
361 parser.add_option( '--increment', dest='increment', type="int", help='How far you move each window while finding chimeric sequences, default is 25' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
362 parser.add_option( '--mask', dest='mask', help='A file containing one sequence you wish to use as a mask for the your sequences' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
363 parser.add_option( '--numwanted', dest='numwanted', type="int", help='How many sequences you would each query sequence compared with' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
364 parser.add_option( '--start', dest='start', type="int", help='Remove sequences that start after thisposition' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
365 parser.add_option( '--end', dest='end', type="int", help='Remove sequences that end before this position' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
366 parser.add_option( '--criteria', dest='criteria', type="int", help='Percentage of sequences to match' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
367 parser.add_option( '--optimize', dest='optimize', help='List of parameters to optimize' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
368 parser.add_option( '--vertical', dest='vertical', help='Ignore any column that only contains gap characters, "-" or "."' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
369 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.' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
370 parser.add_option( '--soft', dest='soft', type='int', help='Soft Mask - percentage required to retain column. (0-100)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
371 parser.add_option( '--hard', dest='hard', help='Hard Column Filter - A file should only contain one line consisting of 0 and 1 chars' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
372 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
373 parser.add_option( '--countends', dest='countends', help='Penalize terminal gaps' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
374 parser.add_option( '--cutoff', dest='cutoff', help='Distance Cutoff threshold, discard larger distances' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
375 parser.add_option( '--countgaps', dest='countgaps', help='count gaps as bases' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
376 parser.add_option( '--output', dest='output', help='Format for output' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
377 parser.add_option( '--method', dest='method', help='Method to use for analysis - cluster' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
378 parser.add_option( '--splitmethod', dest='splitmethod', help='Method to split a distance file - cluster.split' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
379 parser.add_option( '--split', dest='split', help='Chimera split parameter, whether to detect trimeras and quadmeras' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
380 parser.add_option( '--abund', dest='abund', type='int', help='Threshold for rare to Abundant OTU classification' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
381 parser.add_option( '--size', dest='size', type='int', help='Size - sample size' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
382 parser.add_option( '--groupmode', dest='groupmode', help='Collate groups into one result table' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
383 parser.add_option( '--all', dest='all', help='Calculate for all' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
384 parser.add_option( '--freq', dest='freq', type="float", help='Frequency of sequences to choose, as fraction is 0.0 - 1.0 or iteration if int > 1' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
385 parser.add_option( '--iters', dest='iters', type='int', help='Iterations of randomizations' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
386 parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
387 parser.add_option( '--jumble', dest='jumble', help='If false, just a collector curve across the samples' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
388 parser.add_option( '--conservation', dest='conservation', help='Template frequency information' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
389 parser.add_option( '--quantile', dest='quantile', help='Template quantile information' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
390 parser.add_option( '--parents', dest='parents', type='int', help='Number of Parents to investigate' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
391 parser.add_option( '--minsim', dest='minsim', type='int', help='Minimum simarity (0-100 percent)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
392 parser.add_option( '--mincov', dest='mincov', type='int', help='Minimum coverage (0-100 percent)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
393 parser.add_option( '--minbs', dest='minbs', type='int', help='Minimum bootstrap support (0-100 percent)' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
394 parser.add_option( '--minsnp', dest='minsnp', type='int', help='Minimum SNPs to sample(0-100 percent)' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
395 parser.add_option( '--mindim', dest='mindim', type='int', help='Minimum dimensions' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
396 parser.add_option( '--maxdim', dest='maxdim', type='int', help='Maximum dimensions' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
397 parser.add_option( '--percent', dest='percent', type='int', help='(0-100 percent)' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
398 parser.add_option( '--divergence', dest='divergence', type='float', help='Divergence cutoff for chimera determination' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
399 parser.add_option( '--sff', dest='sff', help='Sff file' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
400 parser.add_option( '--svg', dest='svg', help='SVG' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
401 parser.add_option( '--sfftxt', dest='sfftxt', help='Generate a sff.txt file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
402 parser.add_option( '--flow', dest='flow', help='Generate a flowgram file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
403 parser.add_option( '--trim', dest='trim', help='Whether sequences and quality scores are trimmed to the clipQualLeft and clipQualRight values' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
404 parser.add_option( '--input', dest='input', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
405 parser.add_option( '--phylip', dest='phylip', help='' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
406 parser.add_option( '--phylip2', dest='phylip2', help='' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
407 parser.add_option( '--column', dest='column', help='' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
408 parser.add_option( '--sort', dest='sort', help='specify sort order' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
409 parser.add_option( '--sorted', dest='sorted', help='Input is presorted' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
410 parser.add_option( '--showabund', dest='showabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
411 parser.add_option( '--short', dest='short', help='Keep sequences that are too short to chop' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
412 parser.add_option( '--distance', dest='distance', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
413 parser.add_option( '--scale', dest='scale', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
414 parser.add_option( '--numotu', dest='numotu', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
415 parser.add_option( '--fontsize', dest='fontsize', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
416 parser.add_option( '--neqs', dest='neqs', help='' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
417 parser.add_option( '--random', dest='random', help='' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
418 parser.add_option( '--permute', dest='permute', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
419 parser.add_option( '--rarefy', dest='rarefy', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
420 parser.add_option( '--collect', dest='collect', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
421 parser.add_option( '--summary', dest='summary', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
422 parser.add_option( '--large', dest='large', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
423 parser.add_option( '--shuffle', dest='shuffle', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
424 parser.add_option( '--neighbor', dest='neighbor', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
425 parser.add_option( '--expblen', dest='expblen', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
426 parser.add_option( '--expdist', dest='expdist', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
427 parser.add_option( '--ntrees', dest='ntrees', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
428 parser.add_option( '--DNA', dest='DNA', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
429 parser.add_option( '--protein', dest='protein', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
430 parser.add_option( '--kimura', dest='kimura', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
431 parser.add_option( '--jukes', dest='jukes', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
432 parser.add_option( '--matrixout', dest='matrixout', help='' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
433 parser.add_option( '--nseqs', dest='nseqs', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
434 parser.add_option( '--bygroup', dest='bygroup', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
435 parser.add_option( '--design', dest='design', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
436 parser.add_option( '--sets', dest='sets', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
437 parser.add_option( '--metric', dest='metric', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
438 parser.add_option( '--epsilon', dest='epsilon', help='' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
439 parser.add_option( '--alpha', dest='alpha', help='' )
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
440 parser.add_option( '--root', dest='root', help='' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
441 parser.add_option( '--axes', dest='axes', help='table of name column followed by columns of axis values' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
442 parser.add_option( '--numaxes', dest='numaxes', help='the number of axes' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
443 parser.add_option( '--metadata', dest='metadata', help='data table with columns of floating-point values' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
444 parser.add_option( '--basis', dest='basis', help='what the summary file represents' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
445 parser.add_option( '--keepfirst', dest='keepfirst', help='trimming' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
446 parser.add_option( '--removelast', dest='removelast', help='trimming' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
447 parser.add_option( '--persample', dest='persample', help='sub sample option' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
448 parser.add_option( '--timing', dest='timing', help='timing option' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
449 parser.add_option( '--processors', dest='processors', type='int', action='callback', callback=processors_callback, help='Number of processors to use' )
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
450 parser.add_option( '--abskew', dest='abskew', type="float", help='Minimum abundance skew.')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
451 parser.add_option( '--chimealns', dest='chimealns', help='Boolean - produce a file containing multiple alignments of query sequences')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
452 parser.add_option( '--minh', dest='minh', type="float", help='mininum score to report chimera.')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
453 parser.add_option( '--mindiv', dest='mindiv', type="float", help='mininum score to report chimera.')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
454 parser.add_option( '--xn', dest='xn', type="float", help='weight of a no vote')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
455 parser.add_option( '--dn', dest='dn', type="float", help='pseudo-count prior on number of no votes')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
456 parser.add_option( '--xa', dest='xa', type="float", help='weight of an abstain vote')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
457 parser.add_option( '--chunks', dest='chunks', type="int", help='the number of chunks to extract from the query sequence')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
458 parser.add_option( '--minchunk', dest='minchunk', type="int", help='the minimum length of a chunk')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
459 parser.add_option( '--idsmoothwindow', dest='idsmoothwindow', type="int", help='ength of id smoothing window')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
460 parser.add_option( '--minsmoothid', dest='minsmoothid', type="float", help='minimum factional identity over smoothed window')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
461 parser.add_option( '--maxp', dest='maxp', type="int", help='maximum number of candidate parents to consider')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
462 parser.add_option( '--skipgaps', dest='skipgaps', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
463 parser.add_option( '--skipgaps2', dest='skipgaps2', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
464 parser.add_option( '--ucl', dest='ucl', help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
465 parser.add_option( '--queryfract', dest='queryfract', type="float", help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
466 parser.add_option( '--minlen', dest='minlen', type="int", help='Minimun sequence length' )
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
467 parser.add_option( '--maxlen', dest='maxlen', type="int", help='Maximun sequence length' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
468 # include read.otu options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
469 parser.add_option( '--rabund', dest='rabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
470 parser.add_option( '--sabund', dest='sabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
471 parser.add_option( '--shared', dest='shared', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
472 parser.add_option( '--relabund', dest='relabund', help='' )
12
370b3fc4e7d3 Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
Jim Johnson <jj@umn.edu>
parents: 7
diff changeset
473 parser.add_option( '--makerelabund', dest='makerelabund', help='Whether to convert to a relabund file' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
474 parser.add_option( '--ordergroup', dest='ordergroup', help='')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
475 # include read.tree options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
476 parser.add_option( '--tree', dest='tree', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
477
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
478 (options, args) = parser.parse_args()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
479 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
480 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
481 # print >> sys.stderr, options # so will appear as blurb for file
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
482 if options.debug != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
483 debug = options.debug
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
484 params = []
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
485 inputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
486 outputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
487 tmp_dir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
488 tempdefault = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
489 # Report exception if no command is given
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
490 if options.cmd == None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
491 stop_err('No mothur command given')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
492 # Read directory options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
493 if options.tmpdir != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
494 if not os.path.isdir(options.tmpdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
495 os.makedirs(options.tmpdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
496 tmp_dir = options.tmpdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
497 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
498 if options.outputdir != None:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
499 if not os.path.isdir(options.outputdir):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
500 os.makedirs(options.outputdir)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
501 tmp_dir = os.path.join(options.outputdir,'tmp')
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
502 if not os.path.isdir(tmp_dir):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
503 os.makedirs(tmp_dir)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
504 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
505 tmp_dir = tempfile.mkdtemp()
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
506 if options.inputdir != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
507 if not os.path.isdir(options.inputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
508 os.makedirs(options.inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
509 inputdir = options.inputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
510 if options.outputdir != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
511 if not os.path.isdir(options.outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
512 os.makedirs(options.outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
513 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
514 outputdir = os.path.join(tmp_dir,'out')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
515 os.symlink(options.outputdir,outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
516 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
517 print >> sys.stderr, e
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
518 outputdir = options.outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
519 # Set directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
520 if inputdir == None or not os.path.isdir(inputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
521 inputdir = tmp_dir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
522 if outputdir == None or not os.path.isdir(outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
523 outputdir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
524 if options.tempdefault != None and os.path.isdir(options.tempdefault):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
525 tempdefault = ', tempdefault=%s' % options.tempdefault
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
526 # params.append('set.dir(input=%s,output=%s%s)' % (inputdir,outputdir,tempdefault))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
527 params.append('set.dir(output=%s%s)' % (outputdir,tempdefault))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
528 # Check for prerequisite read command
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
529 if options.READ_cmd != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
530 read_cmd_opts = ','.join(get_params(options.READ_cmd,options,inputdir,prefix='READ_'))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
531 params.append('%s(%s)' % (options.READ_cmd,read_cmd_opts))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
532 # Check for command options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
533 cmd_opts = ','.join(get_params(options.cmd,options,inputdir))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
534 # print >> sys.stderr, cmd_opts
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
535 # print >> sys.stderr, params # so will appear as blurb for file
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
536 params.append('%s(%s)' % (options.cmd,cmd_opts))
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
537 if debug: params.append('get.current()')
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
538 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
539 # Generate the mothur commandline
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
540 # http://www.mothur.org/wiki/Command_line_mode
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
541 cmdline = 'mothur "#' + '; '.join(params) + '"'
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
542 if debug: print >> sys.stdout, '%s' % cmdline
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
543 if tmp_dir == None or not os.path.isdir(tmp_dir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
544 tmp_dir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
545 tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
546 tmp_stderr = open( tmp_stderr_name, 'wb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
547 tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
548 tmp_stdout = open( tmp_stdout_name, 'wb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
549 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
550 # proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
551 returncode = proc.wait()
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
552 if debug: print >> sys.stdout, 'returncode %d' % returncode
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
553 tmp_stderr.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
554 # get stderr, allowing for case where it's very large
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
555 tmp_stderr = open( tmp_stderr_name, 'rb' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
556 stderr = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
557 buffsize = 1048576
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
558 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
559 while True:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
560 stderr += tmp_stderr.read( buffsize )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
561 if not stderr or len( stderr ) % buffsize != 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
562 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
563 except OverflowError:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
564 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
565 tmp_stderr.close()
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
566 tmp_stdout.close()
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
567 if debug: print >> sys.stdout, 'parse %s' % tmp_stdout_name
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
568 if returncode != 0:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
569 try:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
570 # try to copy stdout to the logfile
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
571 for output in options.result.split(','):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
572 # Each item has a regex pattern and a file path to a galaxy dataset
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
573 (pattern,path) = output.split(':')
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
574 if debug: print >> sys.stdout, '%s -> %s' % (pattern,path)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
575 if pattern.find('\.logfile') > 0:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
576 if path != None and os.path.exists(path):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
577 logfile_to_html(tmp_stdout_name,path,inputdir,outputdir,title="Mothur %s Error Logfile" % options.cmd)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
578 break
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
579 except:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
580 pass
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
581 raise Exception, stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
582 stdout = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
583 # Parse stdout to provide info
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
584 tmp_stdout = open( tmp_stdout_name, 'rb' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
585 # try to find a "little" something interesting to print as info for the galaxy interface
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
586 info = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
587 if options.cmd.startswith('chimera') and not options.cmd.endswith('check'):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
588 pattern = '^.*$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
589 if options.cmd == 'chimera.slayer':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
590 # gi|11093931|MNE12|AF293003 yes
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
591 pattern = '\S.*\tyes$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
592 elif options.cmd == 'chimera.bellerophon':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
593 # gi|11093939|MNB2|AF293011 is a suspected chimera at breakpoint 2195
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
594 pattern = '\S.* suspected chimera .*'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
595 elif options.cmd == 'chimera.ccode':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
596 # gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
597 pattern = '\S.* chimeric window.*'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
598 elif options.cmd == 'chimera.pintail':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
599 pattern = '\S.*chimera.*Yes'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
600 # move new generated template .freq and .quan files to outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
601 chimera_count = 0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
602 for line in tmp_stdout:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
603 if re.match(pattern,line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
604 chimera_count += 1
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
605 info += "Chimeras: %d" % chimera_count
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
606 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
607 found_begin = False
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
608 info_chars = 0
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
609 for line in tmp_stdout:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
610 if line.find(outputdir) >= 0:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
611 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
612 if line.startswith('**************'):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
613 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
614 if re.match('^Processing.*',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
615 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
616 if re.match('^Reading .*',line):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
617 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
618 if re.match('^Merging .*',line):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
619 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
620 if re.match('^DONE.*',line):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
621 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
622 if re.match('.*\.\.\.\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
623 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
624 if re.match('^\d*\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
625 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
626 # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
627 if not options.cmd.startswith('unifrac') and re.match('^(unique|[0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
628 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
629 if re.match('Output .*',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
630 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
631 if found_begin and info_chars < 200:
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
632 info += "%s" % line
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
633 info_chars += len(line)
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
634 if re.match('mothur > ' + options.cmd + '\(.*\)', line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
635 found_begin = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
636 tmp_stdout.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
637 print >> sys.stdout, info
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
638 # Collect output files
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
639 flist = os.listdir(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
640 if debug: print >> sys.stdout, '%s' % flist
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
641 # chimera.check can generate svg files, but they are not listed in the mothur.*.logfile, so we'll added them in here
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
642 if options.cmd == 'chimera.check':
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
643 svgs = []
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
644 mothurlog = None
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
645 for fname in flist:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
646 if fname.endswith('.svg'):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
647 svgs.append(fname)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
648 elif fname.endswith('.logfile'):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
649 mothurlog = fname
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
650 # process option result first
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
651 # These are the known galaxy datasets listed in the --result= param
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
652 if len(flist) > 0 and options.result:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
653 # items in list are separated by commas
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
654 for output in options.result.split(','):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
655 # Each item has a regex pattern and a file path to a galaxy dataset
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
656 (pattern,path) = output.split(':')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
657 if debug: print >> sys.stdout, '%s -> %s' % (pattern,path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
658 if path == None or path == 'None':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
659 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
660 found = False
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
661 for fname in flist:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
662 if debug: print >> sys.stdout, 'outdir %s match: %s' % (fname,re.match(pattern,fname))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
663 if re.match(pattern,fname):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
664 found = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
665 flist.remove(fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
666 fpath = os.path.join(outputdir,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
667 if fname.endswith('.logfile'):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
668 # Make the logfile into html
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
669 logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd)
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
670 elif outputdir == options.outputdir:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
671 # Use a hard link if outputdir is the extra_files_path, allows link from mothur logfile without copying data.
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
672 try:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
673 if debug: print >> sys.stdout, 'link %s %s' % (fpath, path)
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
674 os.link(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
675 except:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
676 if debug: print >> sys.stdout, 'copy %s %s' % (fpath, path)
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
677 shutil.copy2(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
678 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
679 if debug: print >> sys.stdout, 'copy2 %s %s' % (fpath, path)
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
680 shutil.copy2(fpath, path)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
681 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
682 # mothur.*.logfile may be in tmp_dir
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
683 # chimera.pintail e.g. generates files in the working dir that we might want to save
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
684 if not found:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
685 for fname in os.listdir(tmp_dir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
686 if debug: print >> sys.stdout, 'tmpdir %s match: %s' % (fname,re.match(pattern,fname))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
687 if re.match(pattern,fname):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
688 fpath = os.path.join(tmp_dir,fname)
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
689 if fname.endswith('.logfile'):
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
690 # Make the logfile into html
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
691 logfile_to_html(fpath,path,inputdir,outputdir,title="Mothur %s Logfile" % options.cmd)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
692 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
693 shutil.copy2(fpath, path)
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
694 break
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
695 # Handle the dynamically generated galaxy datasets
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
696 # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
697 # --new_datasets= specifies files to copy to the new_file_path
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
698 # The list items are separated by commas
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
699 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
700 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
701 if options.new_datasets != None and options.new_file_path != None and options.datasetid != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
702 datasets = options.new_datasets.split(',')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
703 for output in options.new_datasets.split(','):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
704 (pattern,ext) = output.split(':');
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
705 for fname in flist:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
706 m = re.match(pattern,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
707 if m:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
708 fpath = os.path.join(outputdir,fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
709 if len(m.groups()) > 0:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
710 # remove underscores since galaxy uses that as a field separator for dynamic datasets
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
711 root = m.groups()[0].replace('_','')
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
712 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
713 # remove the ext from the name if it exists, galaxy will add back later
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
714 # remove underscores since galaxy uses that as a field separator for dynamic datasets
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
715 root = re.sub('\.?'+ext+'$','',fname).replace('_','').replace('.','')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
716 # filename pattern required by galaxy
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
717 fn = "%s_%s_%s_%s_%s" % ( 'primary', options.datasetid, root, 'visible', ext )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
718 if debug: print >> sys.stdout, '> %s' % fpath
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
719 if debug: print >> sys.stdout, '< %s' % os.path.join(options.new_file_path,fn)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
720 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
721 os.link(fpath, os.path.join(options.new_file_path,fn))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
722 except:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
723 shutil.copy2(fpath, os.path.join(options.new_file_path,fn))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
724 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
725 msg = str(e) + stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
726 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
727 if len(msg) < 50 and stdout != None:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
728 # include the last line of stdout
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
729 msg += stdout.splitlines()[-1]
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
730 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
731 stop_err( 'Error running ' + msg)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
732 finally:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
733 # Only remove temporary directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
734 # Enclose in try block, so we don't report error on stale nfs handles
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
735 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
736 if outputdir != options.outputdir and os.path.exists(outputdir):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
737 if os.path.islink(outputdir):
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
738 if debug: print >> sys.stdout, 'rm outputdir %s' % outputdir
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
739 os.remove(outputdir)
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
740 if debug: print >> sys.stdout, 'rmtree outputdir %s' % outputdir
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
741 shutil.rmtree(os.path.dirname(outputdir))
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
742 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
743 if debug: print >> sys.stdout, 'rmtree %s' % outputdir
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
744 shutil.rmtree(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
745 if inputdir != options.inputdir and os.path.exists(inputdir):
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
746 if debug: print >> sys.stdout, 'rmtree %s' % inputdir
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
747 shutil.rmtree(inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
748 except:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
749 if debug: print >> sys.stdout, 'rmtree failed'
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
750 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
751
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
752
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
753 if __name__ == "__main__": __main__()