Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/mothur_wrapper.py @ 27:49058b1f8d3f

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Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author Jim Johnson <jj@umn.edu>
date Tue, 04 Dec 2012 11:05:19 -0600
parents 5c77423823cb
children 7238483c96fa
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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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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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7 mothur v.1.27.0
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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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4f797d3eee3a Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
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49 max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8
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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.perseus'] = dict({'required' : ['fasta','name'], 'optional' : ['group','sigma']})
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189 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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190 cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors']})
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191 cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']})
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192 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']})
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193 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']})
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194 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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195 cmd_dict['classify.tree'] = dict({'required' : ['taxonomy','tree'],'optional' : ['name','group','cutoff']})
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diff changeset
196 #clear.memory ## not needed in galaxy framework
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197 cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']})
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198 cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','count','method','cutoff','hard','precision','sim','showabund','timing']})
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199 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','count','method','cutoff','hard','sim','precision']})
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200 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']})
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201 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors']})
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202 cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']})
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203 cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']})
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7bfe1f843858 Support Mothur v1.20
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diff changeset
204 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']})
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5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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205
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diff changeset
206 cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']})
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diff changeset
207
2
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208 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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diff changeset
209 cmd_dict['count.groups'] = dict({'required' : [['group','shared','count']], 'optional' : ['accnos','groups']})
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210 cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups','large']})
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diff changeset
211
27
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212 cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','contaxonomy'], 'optional' : ['group','label']})
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diff changeset
213
2
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214 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
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215 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []})
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7bfe1f843858 Support Mothur v1.20
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216 cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []})
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217 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']})
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218 cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','subsample','iters','processors']})
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219 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : ['fasta','qfile']})
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220 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']})
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221 cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []})
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222 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']})
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223 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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224 cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
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225 cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
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226 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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227 cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
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228 cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
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229 cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']})
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230 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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231 cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
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232 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
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233 cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
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697156806162 Mothur - update for Mothur version 1.23.0
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diff changeset
234 cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize']})
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235 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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4f797d3eee3a Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
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236 cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
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237 cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
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238 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
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239
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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diff changeset
240 cmd_dict['make.biom'] = dict({'required' : ['shared'] , 'optional' : ['contaxonomy','matrixtype','groups','label']})
27
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diff changeset
241 cmd_dict['make.contigs'] = dict({'required' : ['ffastq','rfastq',], 'optional' : ['align','match','mismatch','gapopen','gapextend','threshold','oligos','bdiffs','pdiffs','tdiffs','processors']})
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242
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diff changeset
243 cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []})
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244 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []})
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245 cmd_dict['make.shared'] = dict({'required' : [['list','group','biom']], 'optional' : ['label','groups']})
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246 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']})
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247 cmd_dict['merge.files'] = dict({'required' : ['input','output']})
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248 cmd_dict['merge.groups'] = dict({'required' : [['shared','group'],'design'], 'optional' : ['groups', 'label']})
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249 cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']})
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250 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
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251 cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']})
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252 cmd_dict['otu.association'] = dict({'required' : [['shared','relabund']], 'optional' : ['groups', 'label','method','metadata']})
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253 cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']})
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254 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
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255 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']})
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256 cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']})
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257 cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']})
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258 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
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259
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260 cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors']})
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261
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262 cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
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263 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
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264 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs','group','processors']})
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265 cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode']})
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266 cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']})
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267 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']})
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268 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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269 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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270 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
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271 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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272 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
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09740be2bc9c Mothur - updates for Mothur version 1.24
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273 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','taxonomy','processors']})
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274 cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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275 cmd_dict['seq.error'] = dict({'required' : ['fasta','reference'] , 'optional' : ['name','qfile','report','ignorechimeras','threshold','processors']})
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276 cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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277 cmd_dict['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','large','processors']})
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278 cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','files']], 'optional' : ['group','sigma','processors']})
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279 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
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280 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']})
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09740be2bc9c Mothur - updates for Mothur version 1.24
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281 cmd_dict['sort.seqs'] = dict({'required' : [['fasta','qfile','name','group','flow','taxonomy']], 'optional' : ['accnos','large']})
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282 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
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283 cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name']})
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284 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
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diff changeset
285 cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
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286 cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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diff changeset
287 cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']})
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parents: 24
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288 cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors']})
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09740be2bc9c Mothur - updates for Mothur version 1.24
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289 cmd_dict['trim.flows'] = dict({'required' : ['flow'], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']})
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parents: 18
diff changeset
290 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','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors']})
26
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291 cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']})
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292 cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']})
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293 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']})
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294 cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']})
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diff changeset
295
0
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296 parser = optparse.OptionParser()
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297 # Options for managing galaxy interaction
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298 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
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299 parser.add_option( '--cmd', dest='cmd', help='The mothur command' )
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300 parser.add_option( '--inputdir', dest='inputdir', help='The directory in which to work' )
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301 parser.add_option( '--outputdir', dest='outputdir', help='The directory in which to work' )
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302 parser.add_option( '--tmpdir', dest='tmpdir', help='The directory in which to work' )
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303 parser.add_option( '--tempdefault', dest='tempdefault', help='The default directory in which to search for input' )
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304 parser.add_option( '--result', dest='result', help='The name pattern and destination for each output file' )
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305 parser.add_option( '--new_file_path', dest='new_file_path', help='The Galaxy new_file_path, dir for extra output datasets' )
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306 parser.add_option( '--datasetid', dest='datasetid', help='The Galaxy new_file_path, dir for extra output datasets' )
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307 parser.add_option( '--new_datasets', dest='new_datasets', help='The name pattern and datatype ext for ouputs' )
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308 # Options for prerequisite Read commands
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309 parser.add_option( '--READ_cmd', dest='READ_cmd', help='The mothur command' )
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310 # required arguments for Read.dist
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311 parser.add_option( '--READ_phylip', dest='READ_phylip', help='' )
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312 parser.add_option( '--READ_column', dest='READ_column', help='' )
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313 # required arguments for Read.otu
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314 parser.add_option( '--READ_rabund', dest='READ_rabund', help='' )
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315 parser.add_option( '--READ_sabund', dest='READ_sabund', help='' )
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316 parser.add_option( '--READ_list', dest='READ_list', help='' )
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317 parser.add_option( '--READ_shared', dest='READ_shared', help='' )
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318 parser.add_option( '--READ_relabund', dest='READ_relabund', help='' )
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319 # required arguments for Read.tree
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320 parser.add_option( '--READ_tree', dest='READ_tree', help='' )
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321 # optional arguments for Read cmds
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322 parser.add_option( '--READ_name', dest='READ_name', help='' )
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323 parser.add_option( '--READ_cutoff', dest='READ_cutoff', type="float", help='' )
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324 parser.add_option( '--READ_hard', dest='READ_hard', help='' )
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325 parser.add_option( '--READ_precision', dest='READ_precision', type="int", help='' )
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326 parser.add_option( '--READ_sim', dest='READ_sim', help='' )
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327 parser.add_option( '--READ_group', dest='READ_group', help='' )
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328 parser.add_option( '--READ_groups', dest='READ_groups', help='' )
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diff changeset
329 parser.add_option( '--READ_ordergroup', dest='READ_ordergroup', help='')
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330 parser.add_option( '--READ_label', dest='READ_label', help='' )
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331 # Parameter specified in mothur
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332 parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' )
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diff changeset
333 parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
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334 parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
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335 parser.add_option( '--ffastq', dest='ffastq', help='forward fastq file' )
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336 parser.add_option( '--rfastq', dest='rfastq', help='reverse fastq file' )
0
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337 parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
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338 parser.add_option( '--repfasta', dest='repfasta', help='fasta file paths' )
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diff changeset
339 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
jjohnson
parents:
diff changeset
340 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
341 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
342 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
343 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
344 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
jjohnson
parents:
diff changeset
345 parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' )
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
346 parser.add_option( '--ignorechimeras', dest='ignorechimeras', help='ignorechimeras' )
0
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( '--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
jjohnson
parents:
diff changeset
348 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
jjohnson
parents:
diff changeset
349 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
jjohnson
parents:
diff changeset
350 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
jjohnson
parents:
diff changeset
351 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
jjohnson
parents:
diff changeset
352 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
jjohnson
parents:
diff changeset
353 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
jjohnson
parents:
diff changeset
354 parser.add_option( '--pdiffs', dest='pdiffs', type="int", help='Number of primer differences to allow' )
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
355 parser.add_option( '--ldiffs', dest='ldiffs', type="int", help='Number of linker sequence differences to allow' )
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
356 parser.add_option( '--sdiffs', dest='sdiffs', type="int", help='Number of spacer sequence differences to allow' )
0
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( '--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
parents:
diff changeset
358 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
parents:
diff changeset
359 parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' )
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
360 parser.add_option( '--keepforward', dest='keepforward', help='T - keep primer' )
0
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( '--name', dest='name', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
362 parser.add_option( '--repname', dest='repname', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
0
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( '--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
parents:
diff changeset
364 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
parents:
diff changeset
365 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
jjohnson
parents:
diff changeset
366 parser.add_option( '--list', dest='list', 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
parents:
diff changeset
367 parser.add_option( '--alignreport', dest='alignreport', help='A align.report file ' )
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
368 parser.add_option( '--report', dest='report', help='' )
0
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( '--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
370 parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
371 parser.add_option( '--contaxonomy', dest='contaxonomy', help='The Taxonomy file output by classify.otu' )
0
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( '--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
373 parser.add_option( '--taxlevel', dest='taxlevel', type="int", help='A Taxonomy level' )
0
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( '--taxon', dest='taxon', action="callback", callback=remove_confidence_callback, help='A Taxon' )
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( '--candidate', dest='candidate', help=' file ' )
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( '--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
377 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
parents:
diff changeset
378 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
jjohnson
parents:
diff changeset
379 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
jjohnson
parents:
diff changeset
380 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
381 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
382 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
383 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
384 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
385 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
386 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
387 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
388 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
389 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
390 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
391 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
392 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
393 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
394 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
395 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
396 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
397 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
398 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
399 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
400 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
401 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
402 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
403 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
404 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
405 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
406 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' )
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
407 parser.add_option( '--count', dest='count', help='Count file' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
408 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
409 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
410 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
411 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
412 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
413 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
414 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
415 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
416 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
417 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
418 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
419 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
420 parser.add_option( '--iters', dest='iters', type='int', help='Iterations of randomizations' )
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
421 parser.add_option( '--maxiter', dest='maxiter', type='int', help='Iterations' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
422 parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
423 parser.add_option( '--subsample', dest='subsample', help='Number of subsample, or T to default to smallest group size' )
0
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( '--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
425 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
426 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
427 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
428 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
429 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
430 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
431 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
432 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
433 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
434 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
435 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
436 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
437 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
438 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
439 parser.add_option( '--flow', dest='flow', help='Generate a flowgram file' )
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
440 parser.add_option( '--minflows', dest='minflows', type='int', help='the minimum number of flows that each sequence must contain' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
441 parser.add_option( '--maxflows', dest='maxflows', type='int', help='the number of flows after which all other flows should be ignored.' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
442 parser.add_option( '--signal', dest='signal', type='float', help='threshold for intensity to be signal' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
443 parser.add_option( '--noise', dest='noise', type='float', help='threshold for intensity to be noise' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
444 parser.add_option( '--mindelta', dest='mindelta', type='float', help='threshold for determining how much change in the flowgram correction' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
445 parser.add_option( '--sigma', dest='sigma', type='float', help='sigma option is used to set the dispersion of the data in the expectation-maximization' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
446 parser.add_option( '--order', dest='order', help='flow order e.g. TACG' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
447 parser.add_option( '--lookup', dest='lookup', help='lookup file that are needed to run shhh.seqs' )
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
448
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
449 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
450 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
451 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
452 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
453 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
454 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
455 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
456 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
457 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
458 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
459 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
460 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
461 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
462 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
463 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
464 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
465 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
466 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
467 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
468 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
469 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
470 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
471 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
472 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
473 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
474 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
475 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
476 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
477 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
478 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
479 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
480 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
481 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
482 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
483 parser.add_option( '--metric', dest='metric', help='' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
484 parser.add_option( '--matrixmodel', dest='matrixmodel', help='' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
485 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
486 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
487 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
488 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
489 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
490 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
491 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
492 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
493 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
494 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
495 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
496 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
497 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
498 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
499 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
500 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
501 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
502 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
503 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
504 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
505 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
506 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
507 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
508 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
509 parser.add_option( '--skipgaps', dest='skipgaps', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
510 parser.add_option( '--skipgaps2', dest='skipgaps2', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
511 parser.add_option( '--ucl', dest='ucl', help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
512 parser.add_option( '--queryfract', dest='queryfract', type="float", help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
513 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
514 parser.add_option( '--maxlen', dest='maxlen', type="int", help='Maximun sequence length' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
515 parser.add_option( '--ecoli', dest='ecoli', help='ecoli referance fasta' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
516 parser.add_option( '--nomatch', dest='nomatch', help='What to with non matching items' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
517 parser.add_option( '--keepprimer', dest='keepprimer', help='Whether to retain the primer' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
518 parser.add_option( '--keepdots', dest='keepdots', help='Whether to retain dots in the sequence' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
519 parser.add_option( '--matrixtype', dest='matrixtype', help='' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
520 parser.add_option( '--consensus', dest='consensus', help='boolean' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
521 parser.add_option( '--biom', dest='biom', help='biom file' )
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
522 parser.add_option( '--classic', dest='classic', help='boolean' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
523 # 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
524 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
525 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
526 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
527 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
528 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
529 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
530 # 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
531 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
532
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
533 (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
534 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
535 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
536 # 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
537 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
538 debug = options.debug
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
539 params = []
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
540 inputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
541 outputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
542 tmp_dir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
543 tempdefault = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
544 # 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
545 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
546 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
547 # Read directory options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
548 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
549 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
550 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
551 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
552 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
553 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
554 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
555 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
556 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
557 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
558 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
559 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
560 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
561 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
562 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
563 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
564 inputdir = options.inputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
565 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
566 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
567 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
568 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
569 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
570 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
571 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
572 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
573 outputdir = options.outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
574 # Set directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
575 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
576 inputdir = tmp_dir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
577 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
578 outputdir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
579 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
580 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
581 # 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
582 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
583 # 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
584 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
585 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
586 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
587 # 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
588 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
589 # 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
590 # 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
591 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
592 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
593 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
594 # 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
595 # 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
596 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
597 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
598 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
599 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
600 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
601 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
602 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
603 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
604 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
605 # 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
606 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
607 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
608 tmp_stderr.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
609 # 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
610 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
611 stderr = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
612 buffsize = 1048576
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
613 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
614 while True:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
615 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
616 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
617 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
618 except OverflowError:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
619 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
620 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
621 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
622 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
623 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
624 try:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
625 # 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
626 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
627 # 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
628 (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
629 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
630 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
631 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
632 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
633 break
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
634 except:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
635 pass
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
636 raise Exception, stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
637 stdout = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
638 # 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
639 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
640 # 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
641 info = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
642 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
643 pattern = '^.*$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
644 if options.cmd == 'chimera.slayer':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
645 # gi|11093931|MNE12|AF293003 yes
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
646 pattern = '\S.*\tyes$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
647 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
648 # 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
649 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
650 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
651 # 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
652 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
653 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
654 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
655 # 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
656 chimera_count = 0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
657 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
658 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
659 chimera_count += 1
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
660 info += "Chimeras: %d" % chimera_count
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
661 elif options.cmd == 'count.groups':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
662 fh = open(os.path.join(outputdir,'tmp.groups.count'),'w')
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
663 for line in tmp_stdout:
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
664 m = re.match('(.+) contains (\d+)\.',line)
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
665 if m and len(m.groups()) == 2:
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
666 info += line
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
667 print >> fh, "%s\t%s\n" % (m.group(1),m.group(2))
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
668 fh.close()
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
669 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
670 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
671 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
672 for line in tmp_stdout:
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
673 if re.match('mothur > ' + options.cmd + '\(.*\)', line):
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
674 found_begin = True
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
675 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
676 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
677 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
678 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
679 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
680 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
681 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
682 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
683 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
684 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
685 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
686 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
687 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
688 if re.match('.*\.\.\.\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
689 continue
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
690 if re.match('^\d*\s*$',line) and not line.find(' contains '):
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
691 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
692 # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
693 if (not (options.cmd.startswith('unifrac') or options.cmd.startswith('count.groups'))
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
694 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
695 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
696 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
697 break
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
698 if re.match('mothur > quit()',line):
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
699 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
700 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
701 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
702 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
703 tmp_stdout.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
704 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
705 # Collect output files
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
706 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
707 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
708 # 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
709 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
710 svgs = []
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
711 mothurlog = None
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
712 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
713 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
714 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
715 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
716 mothurlog = fname
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
717 # 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
718 # 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
719 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
720 # 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
721 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
722 # 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
723 (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
724 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
725 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
726 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
727 found = False
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
728 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
729 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
730 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
731 found = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
732 flist.remove(fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
733 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
734 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
735 # 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
736 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
737 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
738 # 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
739 try:
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, '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
741 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
742 except:
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, '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
744 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
745 else:
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, '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
747 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
748 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
749 # 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
750 # 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
751 if not found:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
752 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
753 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
754 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
755 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
756 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
757 # 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
758 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
759 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
760 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
761 break
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
762 # 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
763 # 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
764 # --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
765 # 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
766 # 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
767 # 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
768 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
769 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
770 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
771 (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
772 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
773 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
774 if m:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
775 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
776 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
777 # 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
778 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
779 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
780 # 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
781 # 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
782 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
783 # 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
784 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
785 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
786 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
787 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
788 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
789 except:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
790 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
791 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
792 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
793 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
794 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
795 # 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
796 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
797 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
798 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
799 finally:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
800 # 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
801 # 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
802 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
803 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
804 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
805 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
806 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
807 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
808 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
809 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
810 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
811 shutil.rmtree(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
812 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
813 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
814 shutil.rmtree(inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
815 except:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
816 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
817 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
818
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
819
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
820 if __name__ == "__main__": __main__()