Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/mothur_wrapper.py @ 18:697156806162

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Mothur - update for Mothur version 1.23.0
author Jim Johnson <jj@umn.edu>
date Tue, 17 Jan 2012 11:22:44 -0600
parents a6189f58fedb
children 09740be2bc9c
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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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697156806162 Mothur - update for Mothur version 1.23.0
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7 mothur v.1.23.0
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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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7bfe1f843858 Support Mothur v1.20
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31 ## Before version 1.18.0 Many mothur commands first required data to be read into memory using: read.otu, read.dist, or read.tree
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32 # This prequisite command and its params are prefixed with 'READ_'
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33 --READ_cmd='read.otu'
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34 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
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35 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
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36 --READ_label='unique,0.07'
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37 """
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38 # import pkg_resources;
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39 import logging, os, string, sys, tempfile, glob, shutil, types, urllib, optparse, re
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40 import shlex, subprocess
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41 from stat import *
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42
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43 log = logging.getLogger( __name__ )
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44
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45 assert sys.version_info[:2] >= ( 2, 4 )
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46
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47 debug = False
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48 #debug = True
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49 max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8
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50
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51 def stop_err( msg ):
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52 sys.stderr.write( "%s\n" % msg )
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53 sys.exit()
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54
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55 def __main__():
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56 # tranform the logfile into html
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57 # add extra file ouput
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58 # add object tags for svg files
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59 def logfile_to_html(logfile_path,htmlfile_path,tmp_input_dir_name,tmp_output_dir_name,title="Mothur Logfile"):
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60 if debug: print >> sys.stdout, 'logfile_to_html %s -> %s' % (logfile_path, htmlfile_path)
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61 if debug: print >> sys.stdout, 'logfile_to_html input_dir: %s' % tmp_input_dir_name
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62 if debug: print >> sys.stdout, 'logfile_to_html output_dir: %s' % tmp_output_dir_name
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63 txt = open(logfile_path,'r')
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64 in_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_input_dir_name) + '/(.+)'
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65 out_pat = re.sub('[^a-zA-Z0-9_/]','.',tmp_output_dir_name) + '/(.+)'
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66 html = open(htmlfile_path,'w')
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67 html.write("<html><head><title>%s</title></head>\n<body>\n<pre>\n" % title)
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68 try:
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69 for line in txt:
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70 if line.find('set.dir') >= 0:
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71 continue
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72 elif line.find('put directory to ') >= 0:
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73 continue
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74 elif line.startswith('Mothur\'s directories:') :
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75 continue
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76 elif line.startswith('outputDir=') :
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77 continue
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78 elif line.startswith('Type ') :
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79 continue
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80 elif line.find(tmp_output_dir_name) >= 0:
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81 # if debug: print >> sys.stdout, 'logfile_to_html #%s#' % line
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82 if line.strip().endswith('.svg'):
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83 line = re.sub(out_pat,' <object id="object" type="image/svg+xml" data="\\1">\\1</object> <br><a href="\\1">\\1</a> <hr/>',line)
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84 else:
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85 line = re.sub(out_pat,'<a href="\\1">\\1</a>',line)
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86 elif line.find(tmp_input_dir_name) >= 0:
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87 line = re.sub(in_pat,'\\1',line)
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88 html.write(line)
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89 except Exception, e:
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90 print(str(e))
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91 pass
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92 html.write('</pre>\n</body>\n</html>\n')
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93 html.close()
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94 #Overide the processors option
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95 def processors_callback(option, opt, value, parser):
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96 val = value if value <= max_processors else max_processors
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97 setattr(parser.values, option.dest, val)
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98 #Strip out "(xx)" confidence values from a taxonomy list
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99 def remove_confidence_callback(option, opt, value, parser):
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100 # val = "'" + re.sub('\(\d+\)','',value) + "'"
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101 setattr(parser.values, option.dest, re.sub('\(\d+\)','',value))
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102 #Mothur separates items in a list of values with hyphens
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103 def multi_val_callback(option, opt, value, parser):
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104 setattr(parser.values, option.dest, '-'.join(value.split(',')))
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105 #Handle list arguments that may contain dataset files
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106 def prepare_input(value,input_dir):
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107 """
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108 Mothur requires items in a list of input values to be separated by hyphens
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109 Change list separator from comma to hyphen
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110 If those items are files, copy them to the input dir.
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111 """
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112 if input_dir != None and value != None and isinstance(value, str):
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113 vals = []
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114 for val in value.split(','):
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115 if val[0] == '/' and os.path.isfile(val):
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116 (dir,fname) = os.path.split(val)
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117 try:
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118 os.symlink(val,os.path.join(input_dir,fname))
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119 except:
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120 shutil.copy(val,os.path.join(input_dir,fname))
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121 vals.append(fname)
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122 if debug: print >> sys.stderr, "scp %s %s" % (val, os.path.join(input_dir,fname))
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123 else:
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124 vals.append(val)
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125 return '-'.join(vals)
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126 return value
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127 #Parse Command Line and get a list of params
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128 # Prefix is used to differentiate between prerequisite commands: read.otu, read.dist, read.tree
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129 def get_params(cmd, options, input_dir, prefix=''):
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130 if debug: print >> sys.stderr, options
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131 params = []
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132 for opt in cmd_dict[cmd]['required']:
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133 if debug: print >> sys.stderr, opt
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134 if isinstance(opt,list): # One of these must be present
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135 missing = True
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136 for sel in opt:
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137 # if debug: print >> sys.stderr, sel
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138 try:
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139 value = prepare_input(getattr(options,prefix+sel), input_dir)
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140 if value != None:
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141 params.append('%s=%s' % (sel,value))
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142 missing = False
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143 except Exception, e:
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144 stop_err('Illegal option for cmd %s : %s %s' % (cmd,sel,e))
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145 if missing:
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146 stop_err('Missing a required parameter for %s, need one of %s' % (cmd,opt))
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147 else: # This option is required
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148 try:
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149 value = prepare_input(getattr(options,prefix+opt), input_dir)
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150 # if debug: print >> sys.stderr, value
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151 if value != None:
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152 params.append('%s=%s' % (opt,value))
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153 else:
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154 stop_err('Missing a required parameter for %s : %s' % (cmd,opt))
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155 except Exception, e:
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156 stop_err('Illegal option %s %s' % (opt,e))
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157 if 'optional' in cmd_dict[cmd]:
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158 for opt in cmd_dict[cmd]['optional']:
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159 # if debug: print >> sys.stderr, opt
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160 try:
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161 value = prepare_input(getattr(options,prefix+opt), input_dir)
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162 # if debug: print >> sys.stderr, value
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163 if value != None:
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164 params.append('%s=%s' % (opt,value))
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165 except Exception, e:
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166 # should distinguish between READ_ opts and cmd opts
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167 # stop_err('Illegal option for %s : %s' % (cmd,opt))
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168 pass
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169 return params
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170 """
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171 The command dict has a dict for each mothur command with required and options arguments
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172 The top level list of required arguments is interpreted that each value item is required and any list item represents a choice of arguments
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173 This covers many, but not all of the argument dependency requirements.
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174 For example - read.dist required a phylip or (column and name) argument.
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175 The complexity of inputs should be handled by the glaxy tool xml file.
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176 """
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177 cmd_dict = dict()
2
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178 cmd_dict['align.check'] = dict({'required' : ['fasta','map']})
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179 cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','save','processors']})
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180 cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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181 cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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182 cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']})
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183 cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']})
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184 #catchall
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185 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
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186 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']})
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187 cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']})
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188 cmd_dict['chimera.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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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 #clear.memory ## not needed in galaxy framework
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196 cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']})
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197 cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','method','cutoff','hard','precision','sim','showabund','timing']})
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198 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','method','cutoff','hard','sim','precision']})
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199 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']})
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200 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','timing','processors']})
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201 cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']})
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202 cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']})
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203 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']})
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204 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
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205 cmd_dict['count.groups'] = dict({'required' : ['group','shared'], 'optional' : ['accnos','groups']})
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206 cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups']})
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207 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
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208 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []})
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209 cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []})
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210 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']})
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211 cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','processors']})
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212 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : []})
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213 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']})
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214 cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []})
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215 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']})
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216 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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217 cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
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218 cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
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219 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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220 cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
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221 cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
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222 cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']})
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223 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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224 cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
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225 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
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226 cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
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227 cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize']})
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228 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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229 cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
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230 cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
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231 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
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232 cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []})
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233 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []})
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234 cmd_dict['make.shared'] = dict({'required' : ['list','group'], 'optional' : ['label','groups']})
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235 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']})
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236 cmd_dict['merge.files'] = dict({'required' : ['input','output']})
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237 cmd_dict['merge.groups'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label']})
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238 cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']})
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239 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
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240 cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']})
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241 cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']})
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parents: 1
diff changeset
242 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
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diff changeset
243 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']})
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diff changeset
244 cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']})
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diff changeset
245 cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']})
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diff changeset
246 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
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7bfe1f843858 Support Mothur v1.20
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parents: 5
diff changeset
247 cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
2
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diff changeset
248 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
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697156806162 Mothur - update for Mothur version 1.23.0
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parents: 15
diff changeset
249 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs','group','processors']})
2
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diff changeset
250 cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']})
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diff changeset
251 cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']})
12
370b3fc4e7d3 Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
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parents: 7
diff changeset
252 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']})
2
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diff changeset
253 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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diff changeset
254 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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diff changeset
255 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
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parents: 1
diff changeset
256 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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diff changeset
257 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
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697156806162 Mothur - update for Mothur version 1.23.0
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parents: 15
diff changeset
258 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport'''taxonomy','processors']})
2
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diff changeset
259 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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parents: 13
diff changeset
260
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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parents: 13
diff changeset
261 cmd_dict['seq.error'] = dict({'required' : ['fasta','reference'] , 'optional' : ['name','qfile','report','ignorechimeras','threshold','processors']})
a6189f58fedb Mothur - updated for Mothur version 1.22.0
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parents: 13
diff changeset
262
2
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diff changeset
263 cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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parents: 13
diff changeset
264
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
265 cmd_dict['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','processors']})
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697156806162 Mothur - update for Mothur version 1.23.0
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parents: 15
diff changeset
266 cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','files']], 'optional' : ['group','sigma','processors']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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parents: 13
diff changeset
267
2
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parents: 1
diff changeset
268 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
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parents: 1
diff changeset
269 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']})
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diff changeset
270 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
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697156806162 Mothur - update for Mothur version 1.23.0
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parents: 15
diff changeset
271 cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name']})
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parents: 1
diff changeset
272 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
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parents: 1
diff changeset
273 cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
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diff changeset
274 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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parents: 13
diff changeset
275 cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']})
2
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diff changeset
276 cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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parents: 13
diff changeset
277 cmd_dict['trim.flows'] = dict({'required' : ['flow'], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']})
13
4f797d3eee3a Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
Jim Johnson <jj@umn.edu>
parents: 12
diff changeset
278 cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents: 1
diff changeset
279 cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
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parents: 1
diff changeset
280 cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
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parents: 1
diff changeset
281 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']})
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697156806162 Mothur - update for Mothur version 1.23.0
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parents: 15
diff changeset
282 cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']})
2
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parents: 1
diff changeset
283
0
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diff changeset
284 parser = optparse.OptionParser()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
285 # Options for managing galaxy interaction
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diff changeset
286 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
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diff changeset
287 parser.add_option( '--cmd', dest='cmd', help='The mothur command' )
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diff changeset
288 parser.add_option( '--inputdir', dest='inputdir', help='The directory in which to work' )
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diff changeset
289 parser.add_option( '--outputdir', dest='outputdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
290 parser.add_option( '--tmpdir', dest='tmpdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
291 parser.add_option( '--tempdefault', dest='tempdefault', help='The default directory in which to search for input' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
292 parser.add_option( '--result', dest='result', help='The name pattern and destination for each output file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
293 parser.add_option( '--new_file_path', dest='new_file_path', help='The Galaxy new_file_path, dir for extra output datasets' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
294 parser.add_option( '--datasetid', dest='datasetid', help='The Galaxy new_file_path, dir for extra output datasets' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
295 parser.add_option( '--new_datasets', dest='new_datasets', help='The name pattern and datatype ext for ouputs' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
296 # Options for prerequisite Read commands
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diff changeset
297 parser.add_option( '--READ_cmd', dest='READ_cmd', help='The mothur command' )
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diff changeset
298 # required arguments for Read.dist
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parents:
diff changeset
299 parser.add_option( '--READ_phylip', dest='READ_phylip', help='' )
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parents:
diff changeset
300 parser.add_option( '--READ_column', dest='READ_column', help='' )
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parents:
diff changeset
301 # required arguments for Read.otu
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parents:
diff changeset
302 parser.add_option( '--READ_rabund', dest='READ_rabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
303 parser.add_option( '--READ_sabund', dest='READ_sabund', help='' )
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parents:
diff changeset
304 parser.add_option( '--READ_list', dest='READ_list', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
305 parser.add_option( '--READ_shared', dest='READ_shared', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff changeset
306 parser.add_option( '--READ_relabund', dest='READ_relabund', help='' )
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parents:
diff changeset
307 # required arguments for Read.tree
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parents:
diff changeset
308 parser.add_option( '--READ_tree', dest='READ_tree', help='' )
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parents:
diff changeset
309 # optional arguments for Read cmds
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diff changeset
310 parser.add_option( '--READ_name', dest='READ_name', help='' )
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parents:
diff changeset
311 parser.add_option( '--READ_cutoff', dest='READ_cutoff', type="float", help='' )
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diff changeset
312 parser.add_option( '--READ_hard', dest='READ_hard', help='' )
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parents:
diff changeset
313 parser.add_option( '--READ_precision', dest='READ_precision', type="int", help='' )
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parents:
diff changeset
314 parser.add_option( '--READ_sim', dest='READ_sim', help='' )
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parents:
diff changeset
315 parser.add_option( '--READ_group', dest='READ_group', help='' )
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parents:
diff changeset
316 parser.add_option( '--READ_groups', dest='READ_groups', help='' )
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parents:
diff changeset
317 parser.add_option( '--READ_ordergroup', dest='READ_ordergroup', help='')
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parents:
diff changeset
318 parser.add_option( '--READ_label', dest='READ_label', help='' )
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parents:
diff changeset
319 # Parameter specified in mothur
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diff changeset
320 parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
321 parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
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parents:
diff changeset
322 parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
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diff changeset
323 parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
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diff changeset
324 parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' )
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diff changeset
325 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
326 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
327 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
328 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
329 parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff changeset
330 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
331 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
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diff changeset
332 parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' )
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diff changeset
333 parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
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parents:
diff changeset
334 parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' )
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diff changeset
335 parser.add_option( '--minlength', dest='minlength', type="int", help='Minimun sequence length' )
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diff changeset
336 parser.add_option( '--maxlength', dest='maxlength', type="int", help='Maximun sequence length' )
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diff changeset
337 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.' )
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diff changeset
338 parser.add_option( '--bdiffs', dest='bdiffs', type="int", help='Number of barcode differences to allow' )
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parents:
diff changeset
339 parser.add_option( '--pdiffs', dest='pdiffs', type="int", help='Number of primer differences to allow' )
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parents:
diff changeset
340 parser.add_option( '--tdiffs', dest='tdiffs', type="int", help='Total number of barcode and primer differences to allow' )
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diff changeset
341 parser.add_option( '--diffs', dest='diffs', type="int", help='Number of mismatched bases to allow between sequences in a group' )
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diff changeset
342 parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' )
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diff changeset
343 parser.add_option( '--name', dest='name', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
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diff changeset
344 parser.add_option( '--accnos', dest='accnos', help='A file containing a list of names' )
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diff changeset
345 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
346 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
347 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
348 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
349 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
350 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
351 parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
352 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
353 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
354 # 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
355 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
356 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
357 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
358 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
359 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
360 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
361 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
362 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
363 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
364 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
365 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
366 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
367 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
368 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
369 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
370 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
371 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
372 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
373 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
374 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
375 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
376 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
377 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
378 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
379 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
380 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
381 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
382 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
383 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
384 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
385 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
386 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
387 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
388 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
389 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
390 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
391 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
392 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
393 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
394 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
395 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
396 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
397 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
398 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
399 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
400 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
401 parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
402 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
403 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
404 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
405 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
406 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
407 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
408 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
409 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
410 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
411 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
412 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
413 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
414 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
415 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
416 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
417 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
418 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
419 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
420 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
421 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
422 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
423 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
424 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
425 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
426
0
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( '--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
428 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
429 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
430 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
431 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
432 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
433 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
434 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
435 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
436 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
437 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
438 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
439 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
440 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
441 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
442 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
443 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
444 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
445 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
446 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
447 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
448 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
449 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
450 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
451 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
452 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
453 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
454 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
455 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
456 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
457 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
458 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
459 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
460 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
461 parser.add_option( '--metric', dest='metric', help='' )
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
462 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
463 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
464 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
465 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
466 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
467 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
468 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
469 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
470 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
471 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
472 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
473 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
474 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
475 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
476 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
477 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
478 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
479 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
480 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
481 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
482 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
483 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
484 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
485 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
486 parser.add_option( '--skipgaps', dest='skipgaps', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
487 parser.add_option( '--skipgaps2', dest='skipgaps2', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
488 parser.add_option( '--ucl', dest='ucl', help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
489 parser.add_option( '--queryfract', dest='queryfract', type="float", help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
490 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
491 parser.add_option( '--maxlen', dest='maxlen', type="int", help='Maximun sequence length' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
492 # 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
493 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
494 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
495 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
496 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
497 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
498 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
499 # 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
500 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
501
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
502 (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
503 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
504 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
505 # 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
506 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
507 debug = options.debug
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
508 params = []
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
509 inputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
510 outputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
511 tmp_dir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
512 tempdefault = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
513 # 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
514 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
515 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
516 # Read directory options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
517 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
518 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
519 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
520 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
521 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
522 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
523 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
524 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
525 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
526 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
527 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
528 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
529 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
530 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
531 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
532 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
533 inputdir = options.inputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
534 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
535 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
536 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
537 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
538 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
539 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
540 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
541 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
542 outputdir = options.outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
543 # Set directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
544 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
545 inputdir = tmp_dir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
546 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
547 outputdir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
548 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
549 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
550 # 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
551 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
552 # 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
553 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
554 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
555 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
556 # 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
557 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
558 # 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
559 # 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
560 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
561 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
562 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
563 # 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
564 # 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
565 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
566 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
567 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
568 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
569 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
570 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
571 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
572 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
573 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
574 # 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
575 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
576 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
577 tmp_stderr.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
578 # 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
579 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
580 stderr = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
581 buffsize = 1048576
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
582 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
583 while True:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
584 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
585 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
586 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
587 except OverflowError:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
588 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
589 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
590 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
591 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
592 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
593 try:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
594 # 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
595 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
596 # 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
597 (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
598 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
599 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
600 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
601 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
602 break
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
603 except:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
604 pass
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
605 raise Exception, stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
606 stdout = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
607 # 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
608 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
609 # 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
610 info = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
611 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
612 pattern = '^.*$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
613 if options.cmd == 'chimera.slayer':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
614 # gi|11093931|MNE12|AF293003 yes
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
615 pattern = '\S.*\tyes$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
616 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
617 # 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
618 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
619 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
620 # 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
621 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
622 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
623 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
624 # 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
625 chimera_count = 0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
626 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
627 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
628 chimera_count += 1
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
629 info += "Chimeras: %d" % chimera_count
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
630 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
631 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
632 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
633 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
634 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
635 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
636 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
637 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
638 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
639 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
640 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
641 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
642 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
643 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
644 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
645 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
646 if re.match('.*\.\.\.\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
647 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
648 if re.match('^\d*\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
649 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
650 # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
651 if not options.cmd.startswith('unifrac') and re.match('^(unique|[0-9.]+)(\t\d+)*',line): # abundance from cluster commands, allow unique line into info
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
652 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
653 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
654 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
655 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
656 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
657 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
658 if re.match('mothur > ' + options.cmd + '\(.*\)', line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
659 found_begin = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
660 tmp_stdout.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
661 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
662 # Collect output files
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
663 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
664 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
665 # 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
666 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
667 svgs = []
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
668 mothurlog = None
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
669 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
670 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
671 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
672 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
673 mothurlog = fname
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
674 # 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
675 # 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
676 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
677 # 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
678 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
679 # 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
680 (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
681 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
682 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
683 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
684 found = False
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
685 for fname in flist:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
686 if debug: print >> sys.stdout, '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
687 if re.match(pattern,fname):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
688 found = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
689 flist.remove(fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
690 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
691 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
692 # 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
693 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
694 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
695 # 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
696 try:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
697 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
698 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
699 except:
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 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
701 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
702 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
703 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
704 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
705 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
706 # 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
707 # 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
708 if not found:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
709 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
710 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
711 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
712 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
713 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
714 # 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
715 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
716 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
717 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
718 break
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
719 # 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
720 # 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
721 # --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
722 # 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
723 # 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
724 # 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
725 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
726 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
727 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
728 (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
729 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
730 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
731 if m:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
732 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
733 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
734 # 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
735 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
736 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
737 # 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
738 # 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
739 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
740 # 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
741 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
742 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
743 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
744 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
745 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
746 except:
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, 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
748 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
749 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
750 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
751 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
752 # 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
753 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
754 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
755 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
756 finally:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
757 # 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
758 # 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
759 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
760 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
761 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
762 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
763 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
764 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
765 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
766 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
767 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
768 shutil.rmtree(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
769 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
770 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
771 shutil.rmtree(inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
772 except:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
773 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
774 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
775
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
776
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
777 if __name__ == "__main__": __main__()