Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/mothur_wrapper.py @ 33:d53b9eb16c2d

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mothur_wrapper.py - convert_value needs to return a String
author Jim Johnson <jj@umn.edu>
date Wed, 11 Sep 2013 16:56:31 -0500
parents ec8df51e841a
children 95d75b35e4d2
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1 #!/usr/bin/env python
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2
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3 """
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4 http://www.mothur.org/
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5
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6 Supports mothur version
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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7 mothur v.1.27.0
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8
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9 Class encapsulating Mothur galaxy tool.
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10 Expect each invocation to include:
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11 Here is an example call to this script with an explanation before each param :
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12 mothur_wrapper.py
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13 # name of a mothur command, this is required
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14 --cmd='summary.shared'
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15 # Galaxy output dataset list, these are output files that can be determined before the command is run
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16 # The items in the list are separated by commas
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17 # Each item contains a regex to match the output filename and a galaxy dataset filepath in which to copy the data (separated by :)
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18 --result='^mothur.\S+\.logfile$:'/home/galaxy/data/database/files/002/dataset_2613.dat,'^\S+\.summary$:'/home/galaxy/data/database/files/002/dataset_2614.dat
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19 # Galaxy output dataset extra_files_path direcotry in which to put all output files
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20 --outputdir='/home/galaxy/data/database/files/002/dataset_2613_files'
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21 # The id of one of the galaxy outputs (e.g. the mothur logfile) used for dynamic dataset generation
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22 # http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
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23 --datasetid='2578'
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24 # The galaxy directory in which to copy all output files for dynamic dataset generation
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25 --new_file_path='/home/galaxy/data/database/tmp'
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26 # specifies files to copy to the new_file_path
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27 # The list is separated by commas
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28 # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :)
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29 # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output
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30 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
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31 ## Before version 1.18.0 Many mothur commands first required data to be read into memory using: read.otu, read.dist, or read.tree
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32 # This prequisite command and its params are prefixed with 'READ_'
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33 --READ_cmd='read.otu'
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34 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
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35 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
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36 --READ_label='unique,0.07'
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37 """
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38 # import pkg_resources;
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39 import logging, os, string, sys, tempfile, glob, shutil, types, urllib, optparse, re
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40 import shlex, subprocess
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41 from stat import *
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42
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43 log = logging.getLogger( __name__ )
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44
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45 assert sys.version_info[:2] >= ( 2, 4 )
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46
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47 debug = False
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48 #debug = True
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49 max_processors = os.getenv('MOTHUR_MAX_PROCESSORS') if os.getenv('MOTHUR_MAX_PROCESSORS') else 8
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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(convert_value(val))
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125 return '-'.join(vals)
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126 return convert_value(value)
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127 # Ensure parameter values are in a format that mothur can handle
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128 def convert_value(value):
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129 """
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130 Convert parameter values to a format suitable for input to mothur
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131 (specifically floating point numbers supplied in scientific
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132 notation)
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133 """
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134 if value is None:
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135 # Return None
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136 x = None
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137 else:
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138 x = str(value)
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139 # Integer
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140 try:
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141 x = int(x)
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142 except ValueError:
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143 # Float
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144 try:
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145 x = float(x)
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146 if str(x).count('e'):
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147 # Ugly hacks to convert scientific notation (which
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148 # mothur can't handle) into decimal format
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149 places = int(str(x).split('e')[1].lstrip('-'))
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150 if x < 1.0:
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151 x = '%.*f' % (int(places),x)
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152 else:
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153 x = '%*.f' % (int(places),x)
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154 except ValueError:
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155 # Neither integer nor float
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156 pass
33
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157 x = str(x)
32
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158 # Return whatever we finished up with
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159 return x
0
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160 #Parse Command Line and get a list of params
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161 # Prefix is used to differentiate between prerequisite commands: read.otu, read.dist, read.tree
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162 def get_params(cmd, options, input_dir, prefix=''):
32
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163 """
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164 Gather parameter values for the specified mothur command 'cmd',
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165 using the definition from the 'cmd_dict' dictionary.
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166 """
0
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167 if debug: print >> sys.stderr, options
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168 params = []
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169 for opt in cmd_dict[cmd]['required']:
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170 if debug: print >> sys.stderr, opt
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171 if isinstance(opt,list): # One of these must be present
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172 missing = True
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173 for sel in opt:
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174 # if debug: print >> sys.stderr, sel
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175 try:
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176 value = prepare_input(getattr(options,prefix+sel), input_dir)
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177 if value != None:
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178 params.append('%s=%s' % (sel,value))
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179 missing = False
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180 except Exception, e:
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181 stop_err('Illegal option for cmd %s : %s %s' % (cmd,sel,e))
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182 if missing:
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183 stop_err('Missing a required parameter for %s, need one of %s' % (cmd,opt))
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184 else: # This option is required
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185 try:
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186 value = prepare_input(getattr(options,prefix+opt), input_dir)
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187 # if debug: print >> sys.stderr, value
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188 if value != None:
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189 params.append('%s=%s' % (opt,value))
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190 else:
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191 stop_err('Missing a required parameter for %s : %s' % (cmd,opt))
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192 except Exception, e:
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193 stop_err('Illegal option %s %s' % (opt,e))
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194 if 'optional' in cmd_dict[cmd]:
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195 for opt in cmd_dict[cmd]['optional']:
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196 # if debug: print >> sys.stderr, opt
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197 try:
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198 value = prepare_input(getattr(options,prefix+opt), input_dir)
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199 # if debug: print >> sys.stderr, value
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200 if value != None:
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201 params.append('%s=%s' % (opt,value))
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202 except Exception, e:
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203 # should distinguish between READ_ opts and cmd opts
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204 # stop_err('Illegal option for %s : %s' % (cmd,opt))
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205 pass
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206 return params
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207 """
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208 The command dict has a dict for each mothur command with required and options arguments
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209 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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210 This covers many, but not all of the argument dependency requirements.
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211 For example - read.dist required a phylip or (column and name) argument.
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212 The complexity of inputs should be handled by the glaxy tool xml file.
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213 """
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214 cmd_dict = dict()
2
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215 cmd_dict['align.check'] = dict({'required' : ['fasta','map']})
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216 cmd_dict['align.seqs'] = dict({'required' : ['fasta','reference',], 'optional' : ['search','ksize','align','match','mismatch','gapopen','gapextend','flip','threshold','save','processors']})
2
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217 cmd_dict['amova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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218 cmd_dict['anosim'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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219 cmd_dict['bin.seqs'] = dict({'required' : ['list','fasta'], 'optional' : ['name','label','group']})
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220 cmd_dict['bootstrap.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','groups','iters','label']})
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221 #catchall
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222 cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
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diff changeset
223 cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']})
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diff changeset
224 cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']})
32
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225 cmd_dict['chimera.perseus'] = dict({'required' : ['fasta','name'], 'optional' : ['group','alpha','beta','cutoff']})
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diff changeset
226 cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']})
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a6189f58fedb Mothur - updated for Mothur version 1.22.0
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diff changeset
227 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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diff changeset
228 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']})
2
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229 cmd_dict['chop.seqs'] = dict({'required' : ['fasta','numbases'], 'optional' : ['countgaps','keep','short']})
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230 cmd_dict['classify.otu'] = dict({'required' : ['list','taxonomy'],'optional' : ['name','cutoff','label','group','probs','basis','reftaxonomy']})
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diff changeset
231 cmd_dict['classify.seqs'] = dict({'required' : ['fasta','reference','taxonomy'],'optional' : ['name','search','ksize','method','match','mismatch','gapopen','gapextend','numwanted','probs','save','processors']})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
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diff changeset
232 cmd_dict['classify.tree'] = dict({'required' : ['taxonomy','tree'],'optional' : ['name','group','cutoff']})
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diff changeset
233 #clear.memory ## not needed in galaxy framework
2
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diff changeset
234 cmd_dict['clearcut'] = dict({'required' : [['phylip','fasta']],'optional' : ['seed','norandom','shuffle','neighbor','expblen','expdist','ntrees','matrixout','kimura','jukes','protein','DNA']})
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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diff changeset
235 cmd_dict['cluster'] = dict({'required' : [['phylip','column']] , 'optional' : ['name','count','method','cutoff','hard','precision','sim','showabund','timing']})
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diff changeset
236 cmd_dict['cluster.classic'] = dict({'required' : ['phylip'] , 'optional' : ['name','count','method','cutoff','hard','sim','precision']})
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diff changeset
237 cmd_dict['cluster.fragments'] = dict({'required' : ['fasta'] , 'optional' : ['name','diffs','percent']})
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49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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diff changeset
238 cmd_dict['cluster.split'] = dict({'required' : [['fasta','phylip','column']] , 'optional' : ['name','count','method','splitmethod','taxonomy','taxlevel','showabund','cutoff','hard','large','precision','classic','timing','processors']})
2
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diff changeset
239 cmd_dict['collect.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','freq','groups','all']})
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240 cmd_dict['collect.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','size','label','freq']})
7
7bfe1f843858 Support Mothur v1.20
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diff changeset
241 cmd_dict['consensus.seqs'] = dict({'required' : ['fasta'], 'optional' : ['list','name','label','cutoff']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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diff changeset
242
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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diff changeset
243 cmd_dict['cooccurrence'] = dict({'required' : ['shared'], 'optional' : ['iters','metric','matrixmodel','groups','label']})
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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diff changeset
244
2
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diff changeset
245 cmd_dict['corr.axes'] = dict({'required' : [['shared','relabund','metadata'],'axes'], 'optional' : ['label','groups','method','numaxes']})
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
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diff changeset
246 cmd_dict['count.groups'] = dict({'required' : [['group','shared','count']], 'optional' : ['accnos','groups']})
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diff changeset
247 cmd_dict['count.seqs'] = dict({'required' : ['name'], 'optional' : ['group','groups','large']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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diff changeset
248
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diff changeset
249 cmd_dict['create.database'] = dict({'required' : [['list','shared'],'repfasta','repname','contaxonomy'], 'optional' : ['group','label']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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diff changeset
250
2
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diff changeset
251 cmd_dict['degap.seqs'] = dict({'required' : ['fasta']})
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252 cmd_dict['deunique.seqs'] = dict({'required' : ['fasta','name'], 'optional' : []})
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diff changeset
253 cmd_dict['deunique.tree'] = dict({'required' : ['tree','name'], 'optional' : []})
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254 cmd_dict['dist.seqs'] = dict({'required' : ['fasta'], 'optional' : ['calc','countends','output','cutoff','oldfasta','column','processors']})
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diff changeset
255 cmd_dict['dist.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','output','subsample','iters','processors']})
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diff changeset
256 cmd_dict['fastq.info'] = dict({'required' : ['fastq'], 'optional' : ['fasta','qfile']})
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257 cmd_dict['filter.seqs'] = dict({'required' : ['fasta'], 'optional' : ['vertical','trump','soft','hard','processors']})
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jjohnson
parents: 1
diff changeset
258 cmd_dict['get.group'] = dict({'required' : ['shared'], 'optional' : []})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
259 cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']})
2
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jjohnson
parents: 1
diff changeset
260 cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
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jjohnson
parents: 1
diff changeset
261 cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
18
697156806162 Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents: 15
diff changeset
262 cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
263 cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
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jjohnson
parents: 1
diff changeset
264 cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
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jjohnson
parents: 1
diff changeset
265 cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
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jjohnson
parents: 1
diff changeset
266 cmd_dict['get.sabund'] = dict({'required' : [['list','rabund']],'optional' : ['label']})
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jjohnson
parents: 1
diff changeset
267 cmd_dict['get.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
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jjohnson
parents: 1
diff changeset
268 cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
269 cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
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jjohnson
parents: 1
diff changeset
270 cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
18
697156806162 Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents: 15
diff changeset
271 cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize']})
2
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jjohnson
parents: 1
diff changeset
272 cmd_dict['homova'] = dict({'required' : ['phylip','design'] , 'optional' : ['alpha','iters']})
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
273 cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
2
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jjohnson
parents: 1
diff changeset
274 cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
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jjohnson
parents: 1
diff changeset
275 cmd_dict['list.seqs'] = dict({'required' : [['fasta','name','group','list','alignreport','taxonomy']]})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
276
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
277 cmd_dict['make.biom'] = dict({'required' : ['shared'] , 'optional' : ['contaxonomy','matrixtype','groups','label']})
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
278 cmd_dict['make.contigs'] = dict({'required' : ['ffastq','rfastq',], 'optional' : ['align','match','mismatch','gapopen','gapextend','threshold','oligos','bdiffs','pdiffs','tdiffs','processors']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
279
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
280 cmd_dict['make.fastq'] = dict({'required' : ['fasta','qfile'] , 'optional' : []})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
281 cmd_dict['make.group'] = dict({'required' : ['fasta','groups'], 'optional' : []})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
282 cmd_dict['make.shared'] = dict({'required' : [['list','group','biom']], 'optional' : ['label','groups']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
283 cmd_dict['mantel'] = dict({'required' : ['phylip','phylip2'] , 'optional' : ['method','iters']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
284 cmd_dict['merge.files'] = dict({'required' : ['input','output']})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
285 cmd_dict['merge.groups'] = dict({'required' : [['shared','group'],'design'], 'optional' : ['groups', 'label']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
286 cmd_dict['metastats'] = dict({'required' : ['shared','design'], 'optional' : ['groups', 'label','iters','threshold','sets','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
287 cmd_dict['nmds'] = dict({'required' : ['phylip'], 'optional' : ['axes','mindim','maxdim','iters','maxiters','epsilon']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
288 cmd_dict['normalize.shared'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','method','norm','groups','makerelabund']})
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
289 cmd_dict['otu.association'] = dict({'required' : [['shared','relabund']], 'optional' : ['groups', 'label','method','metadata']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
290 cmd_dict['otu.hierarchy'] = dict({'required' : ['list','label'], 'optional' : ['output']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
291 cmd_dict['pairwise.seqs'] = dict({'required' : ['fasta'], 'optional' : ['align','calc','countends','output','cutoff','match','mismatch','gapopen','gapextend','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
292 cmd_dict['parse.list'] = dict({'required' : ['list','group'], 'optional' : ['label']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
293 cmd_dict['parsimony'] = dict({'required' : ['tree'], 'optional' : ['group','groups','name','iters','random','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
294 cmd_dict['pca'] = dict({'required' : [['shared','relabund']], 'optional' : ['label','groups','metric']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
295 cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
296
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
297 cmd_dict['pcr.seqs'] = dict({'required' : ['fasta'], 'optional' : ['oligos','name','group','taxonomy','ecoli','start','end','nomatch','keepprimer','keepdots','processors']})
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
298
7
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
299 cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
300 cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
18
697156806162 Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents: 15
diff changeset
301 cmd_dict['pre.cluster'] = dict({'required' : ['fasta'], 'optional' : ['name','diffs','group','processors']})
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
302 cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble','design','sets','groupmode']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
303 cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
304 cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy','design']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
305 cmd_dict['remove.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
306 cmd_dict['remove.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
307 cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
308 cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
309 cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
310 cmd_dict['screen.seqs'] = dict({'required' : ['fasta'], 'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','taxonomy','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
311 cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']})
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
312 cmd_dict['seq.error'] = dict({'required' : ['fasta','reference'] , 'optional' : ['name','qfile','report','ignorechimeras','threshold','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
313 cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
31
a3eed59297ea Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester
Jim Johnson <jj@umn.edu>
parents: 28
diff changeset
314 cmd_dict['shhh.flows'] = dict({'required' : [['flow']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','large','processors']})
a3eed59297ea Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester
Jim Johnson <jj@umn.edu>
parents: 28
diff changeset
315 cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','name']], 'optional' : ['group','sigma','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
316 cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
317 cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
318 cmd_dict['sort.seqs'] = dict({'required' : [['fasta','qfile','name','group','flow','taxonomy']], 'optional' : ['accnos','large']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
319 cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
18
697156806162 Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents: 15
diff changeset
320 cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
321 cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
322 cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
323 cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
15
a6189f58fedb Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents: 13
diff changeset
324 cmd_dict['summary.tax'] = dict({'required' : ['taxonomy'], 'optional' : ['name','group','reftaxonomy']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
325 cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label','subsample','iters','processors']})
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
326 cmd_dict['trim.flows'] = dict({'required' : ['flow'], 'optional' : ['oligos','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','minflows','maxflows','fasta','signal','noise','maxhomop','order','processors']})
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
327 cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','ldiffs','sdiffs','keepforward','allfiles','keepfirst','removelast','processors']})
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
328 cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']})
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
329 cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','subsample','consensus','processors']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
330 cmd_dict['unique.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name']})
18
697156806162 Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents: 15
diff changeset
331 cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']})
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
332
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
333 parser = optparse.OptionParser()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
334 # Options for managing galaxy interaction
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
335 parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
336 parser.add_option( '--cmd', dest='cmd', help='The mothur command' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
337 parser.add_option( '--inputdir', dest='inputdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
338 parser.add_option( '--outputdir', dest='outputdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
339 parser.add_option( '--tmpdir', dest='tmpdir', help='The directory in which to work' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
340 parser.add_option( '--tempdefault', dest='tempdefault', help='The default directory in which to search for input' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
341 parser.add_option( '--result', dest='result', help='The name pattern and destination for each output file' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
342 parser.add_option( '--new_file_path', dest='new_file_path', help='The Galaxy new_file_path, dir for extra output datasets' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
343 parser.add_option( '--datasetid', dest='datasetid', help='The Galaxy new_file_path, dir for extra output datasets' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
344 parser.add_option( '--new_datasets', dest='new_datasets', help='The name pattern and datatype ext for ouputs' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
345 # Options for prerequisite Read commands
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
346 parser.add_option( '--READ_cmd', dest='READ_cmd', help='The mothur command' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
347 # required arguments for Read.dist
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( '--READ_phylip', dest='READ_phylip', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
349 parser.add_option( '--READ_column', dest='READ_column', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
350 # required arguments for Read.otu
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
351 parser.add_option( '--READ_rabund', dest='READ_rabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
352 parser.add_option( '--READ_sabund', dest='READ_sabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
353 parser.add_option( '--READ_list', dest='READ_list', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
354 parser.add_option( '--READ_shared', dest='READ_shared', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
355 parser.add_option( '--READ_relabund', dest='READ_relabund', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
356 # required arguments for Read.tree
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
357 parser.add_option( '--READ_tree', dest='READ_tree', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
358 # optional arguments for Read cmds
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( '--READ_name', dest='READ_name', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
360 parser.add_option( '--READ_cutoff', dest='READ_cutoff', type="float", help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
361 parser.add_option( '--READ_hard', dest='READ_hard', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
362 parser.add_option( '--READ_precision', dest='READ_precision', type="int", help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
363 parser.add_option( '--READ_sim', dest='READ_sim', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
364 parser.add_option( '--READ_group', dest='READ_group', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
365 parser.add_option( '--READ_groups', dest='READ_groups', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
366 parser.add_option( '--READ_ordergroup', dest='READ_ordergroup', help='')
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
367 parser.add_option( '--READ_label', dest='READ_label', help='' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
368 # Parameter specified in mothur
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
369 parser.add_option( '--numbases', dest='numbases', type="int", help='Number of base to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
370 parser.add_option( '--fasta', dest='fasta', help='fasta file paths' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
371 parser.add_option( '--fastq', dest='fastq', help='fastq file paths' )
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
372 parser.add_option( '--ffastq', dest='ffastq', help='forward fastq file' )
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
373 parser.add_option( '--rfastq', dest='rfastq', help='reverse fastq file' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
374 parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
375 parser.add_option( '--repfasta', dest='repfasta', help='fasta file paths' )
0
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( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
377 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
378 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
379 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
380 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
381 parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
382 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
383 parser.add_option( '--ignorechimeras', dest='ignorechimeras', help='ignorechimeras' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
384 parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
385 parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
386 parser.add_option( '--maxhomop', dest='maxhomop', type="int", help='Maximun homopolymer length allowed' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
387 parser.add_option( '--minlength', dest='minlength', type="int", help='Minimun sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
388 parser.add_option( '--maxlength', dest='maxlength', type="int", help='Maximun sequence length' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
389 parser.add_option( '--oligos', dest='oligos', help='The oligos option takes a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier.' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
390 parser.add_option( '--bdiffs', dest='bdiffs', type="int", help='Number of barcode differences to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
391 parser.add_option( '--pdiffs', dest='pdiffs', type="int", help='Number of primer differences to allow' )
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
392 parser.add_option( '--ldiffs', dest='ldiffs', type="int", help='Number of linker sequence differences to allow' )
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
393 parser.add_option( '--sdiffs', dest='sdiffs', type="int", help='Number of spacer sequence differences to allow' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
394 parser.add_option( '--tdiffs', dest='tdiffs', type="int", help='Total number of barcode and primer differences to allow' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
395 parser.add_option( '--diffs', dest='diffs', type="int", help='Number of mismatched bases to allow between sequences in a group' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
396 parser.add_option( '--allfiles', dest='allfiles', help='T - generate fasta and group for each barcode' )
24
09740be2bc9c Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 18
diff changeset
397 parser.add_option( '--keepforward', dest='keepforward', help='T - keep primer' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
398 parser.add_option( '--name', dest='name', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
399 parser.add_option( '--repname', dest='repname', help='A file containing a 2 column table: name, and comma separated list of represetatives' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
400 parser.add_option( '--accnos', dest='accnos', help='A file containing a list of names' )
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
401 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
402 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
403 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
404 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
405 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
406 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
407 parser.add_option( '--reftaxonomy', dest='reftaxonomy', help='A Taxonomy file' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
408 parser.add_option( '--contaxonomy', dest='contaxonomy', help='The Taxonomy file output by classify.otu' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
409 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
410 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
411 # 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
412 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
413 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
414 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
415 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
416 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
417 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
418 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
419 parser.add_option( '--align', dest='align', help='Alignment method: needleman, blastn, gotoh' )
31
a3eed59297ea Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester
Jim Johnson <jj@umn.edu>
parents: 28
diff changeset
420 parser.add_option( '--match', dest='match', help='Reward for a match, default is +1.0' )
a3eed59297ea Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester
Jim Johnson <jj@umn.edu>
parents: 28
diff changeset
421 parser.add_option( '--mismatch', dest='mismatch', help='Penalty for a mismatch, default is -1.0' )
28
7238483c96fa mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer
Jim Johnson <jj@umn.edu>
parents: 27
diff changeset
422 parser.add_option( '--gapopen', dest='gapopen', help='Penalty for a opening, default is -2.0' )
7238483c96fa mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer
Jim Johnson <jj@umn.edu>
parents: 27
diff changeset
423 parser.add_option( '--gapextend', dest='gapextend', help='Penalty for extending a gap, default is -1.0' )
7238483c96fa mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer
Jim Johnson <jj@umn.edu>
parents: 27
diff changeset
424 parser.add_option( '--precision', dest='precision', help='' )
7238483c96fa mothur_wrapper.py - remove type restrictions for params - was failing for chimera.slayer
Jim Johnson <jj@umn.edu>
parents: 27
diff changeset
425 parser.add_option( '--threshold', dest='threshold', 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
426 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
427 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
428 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
429 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
430 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
431 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
432 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
433 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
434 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
435 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
436 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
437 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
438 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
439 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
440 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
441 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
442 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
443 parser.add_option( '--calc', dest='calc', help='Calc Method - Gap Penality' )
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
444 parser.add_option( '--count', dest='count', help='Count file' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
445 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
446 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
447 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
448 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
449 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
450 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
451 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
452 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
453 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
454 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
455 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
456 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
457 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
458 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
459 parser.add_option( '--maxiters', dest='maxiters', type='int', help='Iterations of randomizations' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
460 parser.add_option( '--subsample', dest='subsample', help='Number of subsample, or T to default to smallest group size' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
461 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
462 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
463 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
464 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
465 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
466 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
467 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
468 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
469 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
470 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
471 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
472 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
473 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
474 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
475 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
476 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
477 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
478 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
479 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
480 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
481 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
482 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
483 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
484 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
485
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
486 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
487 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
488 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
489 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
490 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
491 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
492 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
493 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
494 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
495 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
496 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
497 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
498 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
499 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
500 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
501 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
502 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
503 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
504 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
505 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
506 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
507 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
508 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
509 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
510 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
511 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
512 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
513 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
514 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
515 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
516 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
517 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
518 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
519 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
520 parser.add_option( '--metric', dest='metric', help='' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
521 parser.add_option( '--matrixmodel', dest='matrixmodel', help='' )
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
522 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
523 parser.add_option( '--alpha', dest='alpha', help='' )
32
ec8df51e841a Fixes courtesy of Peter Briggs:
Jim Johnson <jj@umn.edu>
parents: 31
diff changeset
524 parser.add_option( '--beta', dest='beta', help='' )
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
525 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
526 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
527 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
528 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
529 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
530 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
531 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
532 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
533 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
534 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
535 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
536 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
537 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
538 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
539 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
540 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
541 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
542 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
543 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
544 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
545 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
546 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
547 parser.add_option( '--skipgaps', dest='skipgaps', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
548 parser.add_option( '--skipgaps2', dest='skipgaps2', help='Boolean')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
549 parser.add_option( '--ucl', dest='ucl', help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
550 parser.add_option( '--queryfract', dest='queryfract', type="float", help='')
7bfe1f843858 Support Mothur v1.20
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
551 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
552 parser.add_option( '--maxlen', dest='maxlen', type="int", help='Maximun sequence length' )
26
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
553 parser.add_option( '--ecoli', dest='ecoli', help='ecoli referance fasta' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
554 parser.add_option( '--nomatch', dest='nomatch', help='What to with non matching items' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
555 parser.add_option( '--keepprimer', dest='keepprimer', help='Whether to retain the primer' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
556 parser.add_option( '--keepdots', dest='keepdots', help='Whether to retain dots in the sequence' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
557 parser.add_option( '--matrixtype', dest='matrixtype', help='' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
558 parser.add_option( '--consensus', dest='consensus', help='boolean' )
5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents: 24
diff changeset
559 parser.add_option( '--biom', dest='biom', help='biom file' )
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
560 parser.add_option( '--classic', dest='classic', help='boolean' )
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
561 # 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
562 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
563 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
564 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
565 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
566 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
567 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
568 # 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
569 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
570
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
571 (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
572 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
573 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
574 # 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
575 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
576 debug = options.debug
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
577 params = []
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
578 inputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
579 outputdir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
580 tmp_dir = None
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
581 tempdefault = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
582 # 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
583 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
584 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
585 # Read directory options
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
586 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
587 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
588 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
589 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
590 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
591 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
592 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
593 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
594 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
595 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
596 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
597 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
598 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
599 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
600 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
601 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
602 inputdir = options.inputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
603 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
604 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
605 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
606 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
607 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
608 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
609 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
610 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
611 outputdir = options.outputdir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
612 # Set directories
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
613 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
614 inputdir = tmp_dir
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
615 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
616 outputdir = tempfile.mkdtemp()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
617 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
618 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
619 # 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
620 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
621 # 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
622 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
623 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
624 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
625 # 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
626 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
627 # 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
628 # 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
629 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
630 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
631 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
632 # 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
633 # 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
634 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
635 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
636 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
637 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
638 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
639 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
640 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
641 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
642 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
643 # 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
644 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
645 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
646 tmp_stderr.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
647 # 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
648 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
649 stderr = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
650 buffsize = 1048576
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
651 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
652 while True:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
653 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
654 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
655 break
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
656 except OverflowError:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
657 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
658 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
659 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
660 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
661 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
662 try:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
663 # 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
664 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
665 # 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
666 (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
667 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
668 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
669 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
670 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
671 break
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
672 except:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
673 pass
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
674 raise Exception, stderr
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
675 stdout = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
676 # 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
677 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
678 # 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
679 info = ''
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
680 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
681 pattern = '^.*$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
682 if options.cmd == 'chimera.slayer':
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
683 # gi|11093931|MNE12|AF293003 yes
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
684 pattern = '\S.*\tyes$'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
685 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
686 # 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
687 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
688 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
689 # 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
690 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
691 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
692 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
693 # 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
694 chimera_count = 0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
695 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
696 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
697 chimera_count += 1
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
698 info += "Chimeras: %d" % chimera_count
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
699 elif options.cmd == 'count.groups':
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
700 fh = open(os.path.join(outputdir,'tmp.groups.count'),'w')
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
701 for line in tmp_stdout:
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
702 m = re.match('(.+) contains (\d+)\.',line)
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
703 if m and len(m.groups()) == 2:
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
704 info += line
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
705 print >> fh, "%s\t%s\n" % (m.group(1),m.group(2))
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
706 fh.close()
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
707 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
708 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
709 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
710 for line in tmp_stdout:
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
711 if re.match('mothur > ' + options.cmd + '\(.*\)', line):
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
712 found_begin = True
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
713 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
714 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
715 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
716 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
717 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
718 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
719 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
720 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
721 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
722 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
723 continue
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
724 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
725 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
726 if re.match('.*\.\.\.\s*$',line):
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
727 continue
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
728 if re.match('^\d*\s*$',line) and not line.find(' contains '):
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
729 continue
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
730 # if re.match('^(unique|[0-9.]*)(\t\d+)+',line): # abundance from cluster commands
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
731 if (not (options.cmd.startswith('unifrac') or options.cmd.startswith('count.groups'))
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
732 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
733 continue
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
734 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
735 break
27
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
736 if re.match('mothur > quit()',line):
49058b1f8d3f Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents: 26
diff changeset
737 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
738 if 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
739 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
740 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
741 tmp_stdout.close()
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
742 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
743 # Collect output files
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
744 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
745 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
746 # 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
747 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
748 svgs = []
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
749 mothurlog = None
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
750 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
751 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
752 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
753 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
754 mothurlog = fname
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
755 # 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
756 # 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
757 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
758 # 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
759 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
760 # 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
761 (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
762 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
763 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
764 continue
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
765 found = False
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
766 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
767 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
768 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
769 found = True
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
770 flist.remove(fname)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
771 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
772 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
773 # 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
774 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
775 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
776 # 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
777 try:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
778 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
779 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
780 except:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
781 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
782 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
783 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
784 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
785 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
786 break
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
787 # 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
788 # 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
789 if not found:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
790 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
791 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
792 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
793 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
794 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
795 # 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
796 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
797 else:
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
798 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
799 break
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
800 # 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
801 # 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
802 # --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
803 # 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
804 # 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
805 # 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
806 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
807 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
808 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
809 (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
810 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
811 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
812 if m:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
813 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
814 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
815 # 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
816 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
817 else:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
818 # 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
819 # 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
820 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
821 # 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
822 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
823 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
824 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
825 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
826 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
827 except:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
828 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
829 except Exception, e:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
830 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
831 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
832 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
833 # 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
834 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
835 """
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
836 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
837 finally:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
838 # 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
839 # 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
840 try:
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
841 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
842 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
843 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
844 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
845 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
846 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
847 else:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
848 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
849 shutil.rmtree(outputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
850 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
851 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
852 shutil.rmtree(inputdir)
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
853 except:
2
e990ac8a0f58 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
854 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
855 pass
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
856
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
857
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
858 if __name__ == "__main__": __main__()