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1 # teste_out/teste_out.py - a self annotated version of rgToolFactory2.py generated by running rgToolFactory2.py
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2 # to make a new Galaxy tool called teste_out
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3 # User bioinfolucas@gmail.com at 12/03/2015 17:34:22
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4 # rgToolFactoryMultIn.py
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5 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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6 #
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7 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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8 #
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9 # all rights reserved
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10 # Licensed under the LGPL
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11 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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12 #
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13 # January 2015
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14 # unified all setups by passing the script on the cl rather than via a PIPE - no need for treat_bash_special so removed
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15 #
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16 # in the process of building a complex tool
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17 # added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package
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18 # add that package to tool_dependencies
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19 # Note that once the generated tool is loaded, it will have that package's env.sh loaded automagically so there is no
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20 # --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.
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21 #
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22 # sept 2014 added additional params from
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23 # https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default
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24 # passing them is complex
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25 # and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on
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26 # the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script
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27 # see examples on this tool form
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28
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29 # august 2014
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30
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31 # Allows arbitrary number of input files
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32 # NOTE positional parameters are now passed to script
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33 # and output (may be "None") is *before* arbitrary number of inputs
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34 #
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35 # march 2014
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36 # had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
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37 # grrrrr - night before a demo
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38 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
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39 #
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40 # added ghostscript and graphicsmagick as dependencies
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41 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
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42 # errors ensued
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43 #
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44 # august 2013
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45 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
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46 #
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47 # july 2013
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48 # added ability to combine images and individual log files into html output
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49 # just make sure there's a log file foo.log and it will be output
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50 # together with all images named like "foo_*.pdf
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51 # otherwise old format for html
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52 #
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53 # January 2013
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54 # problem pointed out by Carlos Borroto
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55 # added escaping for <>$ - thought I did that ages ago...
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56 #
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57 # August 11 2012
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58 # changed to use shell=False and cl as a sequence
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59
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60 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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61 # It also serves as the wrapper for the new tool.
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62 #
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63 # you paste and run your script
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64 # Only works for simple scripts that read one input from the history.
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65 # Optionally can write one new history dataset,
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66 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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67
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68 # DO NOT install on a public or important site - please.
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69
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70 # installed generated tools are fine if the script is safe.
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71 # They just run normally and their user cannot do anything unusually insecure
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72 # but please, practice safe toolshed.
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73 # Read the fucking code before you install any tool
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74 # especially this one
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75
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76 # After you get the script working on some test data, you can
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77 # optionally generate a toolshed compatible gzip file
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78 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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79 # safe and largely automated installation in a production Galaxy.
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80
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81 # If you opt for an HTML output, you get all the script outputs arranged
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82 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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83 # Ugly but really inexpensive.
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84 #
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85 # Patches appreciated please.
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86 #
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87 #
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88 # long route to June 2012 product
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89 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
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90 # derived from an integrated script model
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91 # called rgBaseScriptWrapper.py
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92 # Note to the unwary:
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93 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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94 # There is nothing stopping a malicious user doing whatever they choose
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95 # Extremely dangerous!!
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96 # Totally insecure. So, trusted users only
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97 #
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98 # preferred model is a developer using their throw away workstation instance - ie a private site.
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99 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
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100 #
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101
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102 import sys
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103 import shutil
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104 import subprocess
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105 import os
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106 import time
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107 import tempfile
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108 import optparse
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109 import tarfile
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110 import re
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111 import shutil
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112 import math
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113
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114 progname = os.path.split(sys.argv[0])[1]
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115 myversion = 'V001.1 March 2014'
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116 verbose = False
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117 debug = False
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118 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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119
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120 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
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121 # tool xml
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122
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123 def timenow():
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124 """return current time as a string
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125 """
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126 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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127
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128 def quote_non_numeric(s):
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129 """return a prequoted string for non-numerics
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130 useful for perl and Rscript parameter passing?
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131 """
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132 try:
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133 res = float(s)
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134 return s
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135 except ValueError:
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136 return '"%s"' % s
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137
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138 html_escape_table = {
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139 "&": "&",
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140 ">": ">",
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141 "<": "<",
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142 "$": "\$"
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143 }
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144
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145 def html_escape(text):
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146 """Produce entities within text."""
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147 return "".join(html_escape_table.get(c,c) for c in text)
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148
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149
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150 def html_unescape(text):
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151 """Revert entities within text."""
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152 t = text.replace('&','&').replace('>','>').replace('<','<').replace('\$','$')
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153 return t
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154
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155 def cmd_exists(cmd):
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156 return subprocess.call("type " + cmd, shell=True,
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157 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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158
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159 def parse_citations(citations_text):
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160 """
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161 """
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162 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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163 citation_tuples = []
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164 for citation in citations:
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165 if citation.startswith("doi"):
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166 citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
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167 else:
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168 citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
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169 return citation_tuples
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170
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171 def shell_source(script):
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172 """need a way to source a Galaxy tool interpreter env.sh to point at the right dependency package
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173 This based on the idea in http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html
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174 Note that we have to finesse any wierdly quoted newlines in automagic exports using nulls (env -0) as newlines"""
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175 pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True)
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176 output = pipe.communicate()[0]
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177 outl = output.split('\0')
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178 outl = [x for x in outl if len(x.split("=")) == 2]
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179 newenv = dict((line.split("=", 1) for line in outl))
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180 os.environ.update(newenv)
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181
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182 class ScriptRunner:
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183 """class is a wrapper for an arbitrary script
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184 note funky templating. this should all be done proper.
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185 Problem is, this kludge developed quite naturally and seems to work ok with
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186 little overhead...
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187
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188 """
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189
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190
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191 def __init__(self,opts=None):
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192 """
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193 cleanup inputs, setup some outputs
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194
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195 """
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196
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197 self.toolhtmldepinterpskel = """<?xml version="1.0"?>
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198 <tool_dependency>
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199 <package name="ghostscript" version="9.10">
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200 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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201 </package>
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202 <package name="graphicsmagick" version="1.3.18">
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203 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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204 </package>
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205 <package name="%(interpreter_name)s" version="%(interpreter_version)s">
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206 <repository name="%(interpreter_pack)s" owner="%(interpreter_owner)s" prior_installation_required="True" />
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207 </package>
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208
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209 <readme>
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210 %(readme)s
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211 This file was autogenerated by the Galaxy Tool Factory 2
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212 </readme>
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213 </tool_dependency>
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214 """
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215
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216 self.toolhtmldepskel = """<?xml version="1.0"?>
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217 <tool_dependency>
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218 <package name="ghostscript" version="9.10">
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219 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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220 </package>
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221 <package name="graphicsmagick" version="1.3.18">
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222 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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223 </package>
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224 <readme>
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225 %(readme)s
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226 This file was autogenerated by the Galaxy Tool Factory 2
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227 </readme>
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228 </tool_dependency>
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229 """
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230
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231 self.emptytoolhtmldepskel = """<?xml version="1.0"?>
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232 <tool_dependency>
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233 <readme>
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234 %(readme)s
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235 This file was autogenerated by the Galaxy Tool Factory 2
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236 </readme>
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237 </tool_dependency>
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238 """
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239
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240 self.protorequirements = """<requirements>
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241 <requirement type="package" version="9.10">ghostscript</requirement>
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242 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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243 </requirements>"""
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244
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245 self.protorequirements_interpreter = """<requirements>
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246 <requirement type="package" version="9.10">ghostscript</requirement>
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247 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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248 <requirement type="package" version="%(interpreter_version)s">%(interpreter_name)s</requirement>
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249 </requirements>"""
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250
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251
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252 self.newCommand="""
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253 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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254 --tool_name "%(toolname)s"
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255 %(command_inputs)s
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256 %(command_outputs)s
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257 """
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258
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259 self.tooltestsTabOnly = """
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260 <test>
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261 %(test1Inputs)s
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262 <param name="job_name" value="test1"/>
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263 <param name="runMe" value="$runMe"/>
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264 <output name="output1="%(test1Output)s" ftype="tabular"/>
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265 %(additionalParams)s
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266 </test>
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267 """
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268
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269 self.tooltestsHTMLOnly = """
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270 <test>
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271 %(test1Inputs)s
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272 <param name="job_name" value="test1"/>
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273 <param name="runMe" value="$runMe"/>
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274 %(additionalParams)s
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275 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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276 </test>
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277 """
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278
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279 self.tooltestsBoth = """
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280 <test>
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281 %(test1Inputs)s
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282 <param name="job_name" value="test1"/>
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283 <param name="runMe" value="$runMe"/>
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284 %(additionalParams)s
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285 <output name="output1" file="%(test1Output)s" ftype="tabular" />
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286 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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287 </test>
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288 """
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289
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290 self.newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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291 %(tooldesc)s
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292 %(requirements)s
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293 <command interpreter="python">
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294 %(command)s
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295 </command>
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296 <inputs>
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297 %(inputs)s
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298 %(additionalInputs)s
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299 </inputs>
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300 <outputs>
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301 %(outputs)s
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302 </outputs>
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303 <configfiles>
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304 <configfile name="runMe">
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305 %(script)s
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306 </configfile>
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307 </configfiles>
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308 <tests>
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309 %(tooltests)s
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310 </tests>
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311 <help>
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312
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313 %(help)s
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314
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315 This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
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316 https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
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317 </help>
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318 <citations>
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319 %(citations)s
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320 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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321 </citations>
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322 </tool>"""
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323
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324 self.useGM = cmd_exists('gm')
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325 self.useIM = cmd_exists('convert')
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326 self.useGS = cmd_exists('gs')
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327 self.temp_warned = False # we want only one warning if $TMP not set
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328 if opts.output_dir: # simplify for the tool tarball
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329 os.chdir(opts.output_dir)
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330 self.thumbformat = 'png'
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331 self.opts = opts
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332 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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333 self.toolid = self.toolname
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334 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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335 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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336 self.xmlfile = '%s.xml' % self.toolname
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337 rx = open(self.opts.script_path,'r').readlines()
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338 rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed
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339 self.script = '\n'.join(rx)
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340 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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341 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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342 tscript.write(self.script)
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343 tscript.close()
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344 self.indentedScript = " %s" % '\n'.join([' %s' % html_escape(x) for x in rx]) # for restructured text in help
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345 self.escapedScript = "%s" % '\n'.join([' %s' % html_escape(x) for x in rx])
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346 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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347 if opts.output_dir: # may not want these complexities
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348 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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349 art = '%s.%s' % (self.toolname,opts.interpreter)
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350 artpath = os.path.join(self.opts.output_dir,art) # need full path
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351 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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352 artifact.write(self.script)
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353 artifact.close()
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354 self.cl = []
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355 self.html = []
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356 self.test1Inputs = [] # now a list
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357 a = self.cl.append
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358 a(opts.interpreter)
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359 a(self.sfile)
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360 # if multiple inputs - positional or need to distinguish them with cl params
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361 if opts.input_tab:
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362 tests = []
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363 for i,intab in enumerate(opts.input_tab): # if multiple, make tests
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364 if intab.find(',') <> -1:
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365 (gpath,uname) = intab.split(',')
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366 else:
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367 gpath = uname = intab
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368 tests.append(os.path.basename(gpath))
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369 self.test1Inputs = '<param name="input_tab" value="%s" />' % (','.join(tests))
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370 else:
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371 self.test1Inputs = ''
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372 # we always pass path,name pairs in using python optparse append
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373 # but the command line has to be different
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374 self.infile_paths = ''
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375 self.infile_names = ''
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376 if self.opts.input_tab:
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377 self.infile_paths = ','.join([x.split(',')[0].strip() for x in self.opts.input_tab])
|
|
|
378 self.infile_names = ','.join([x.split(',')[1].strip() for x in self.opts.input_tab])
|
|
|
379 if self.opts.interpreter == 'python':
|
|
|
380 # yes, this is how additional parameters are always passed in python - to the TF itself and to
|
|
|
381 # scripts to avoid having unknown parameter names (yes, they can be parsed but...) on the command line
|
|
|
382 if self.opts.input_tab:
|
|
|
383 a('--inpaths=%s' % (self.infile_paths))
|
|
|
384 a('--innames=%s' % (self.infile_names))
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|
|
385 if self.opts.output_tab:
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|
386 a('--outpath=%s' % self.opts.output_tab)
|
|
|
387 for p in opts.additional_parameters:
|
|
|
388 p = p.replace('"','')
|
|
|
389 psplit = p.split(',')
|
|
|
390 param = html_unescape(psplit[0])
|
|
|
391 value = html_unescape(psplit[1])
|
|
|
392 a('%s="%s"' % (param,value))
|
|
|
393 if (self.opts.interpreter == 'Rscript'):
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|
|
394 # pass params on command line as expressions which the script evaluates - see sample
|
|
|
395 if self.opts.input_tab:
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|
|
396 a('INPATHS="%s"' % self.infile_paths)
|
|
|
397 a('INNAMES="%s"' % self.infile_names)
|
|
|
398 if self.opts.output_tab:
|
|
|
399 a('OUTPATH="%s"' % self.opts.output_tab)
|
|
|
400 for p in opts.additional_parameters:
|
|
|
401 p = p.replace('"','')
|
|
|
402 psplit = p.split(',')
|
|
|
403 param = html_unescape(psplit[0])
|
|
|
404 value = html_unescape(psplit[1])
|
|
|
405 a('%s=%s' % (param,quote_non_numeric(value)))
|
|
|
406 if (self.opts.interpreter == 'perl'):
|
|
|
407 # pass positional params on command line - perl script needs to discombobulate the path/name lists
|
|
|
408 if self.opts.input_tab:
|
|
|
409 a('%s' % self.infile_paths)
|
|
|
410 a('%s' % self.infile_names)
|
|
|
411 if self.opts.output_tab:
|
|
|
412 a('%s' % self.opts.output_tab)
|
|
|
413 for p in opts.additional_parameters:
|
|
|
414 # followed by any additional name=value parameter pairs
|
|
|
415 p = p.replace('"','')
|
|
|
416 psplit = p.split(',')
|
|
|
417 param = html_unescape(psplit[0])
|
|
|
418 value = html_unescape(psplit[1])
|
|
|
419 a('%s=%s' % (param,quote_non_numeric(value)))
|
|
|
420 if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
|
|
|
421 # more is better - now move all params into environment AND drop on to command line.
|
|
|
422 self.cl.insert(0,'env')
|
|
|
423 if self.opts.input_tab:
|
|
|
424 self.cl.insert(1,'INPATHS=%s' % (self.infile_paths))
|
|
|
425 self.cl.insert(2,'INNAMES=%s' % (self.infile_names))
|
|
|
426 if self.opts.output_tab:
|
|
|
427 self.cl.insert(3,'OUTPATH=%s' % (self.opts.output_tab))
|
|
|
428 a('OUTPATH=%s' % (self.opts.output_tab))
|
|
|
429 # sets those environment variables for the script
|
|
|
430 # additional params appear in CL - yes, it's confusing
|
|
|
431 for i,p in enumerate(opts.additional_parameters):
|
|
|
432 psplit = p.split(',')
|
|
|
433 param = html_unescape(psplit[0])
|
|
|
434 value = html_unescape(psplit[1])
|
|
|
435 a('%s=%s' % (param,quote_non_numeric(value)))
|
|
|
436 self.cl.insert(4+i,'%s=%s' % (param,quote_non_numeric(value)))
|
|
|
437 self.interpreter_owner = 'SYSTEM'
|
|
|
438 self.interpreter_pack = 'SYSTEM'
|
|
|
439 self.interpreter_name = 'SYSTEM'
|
|
|
440 self.interpreter_version = 'SYSTEM'
|
|
|
441 self.interpreter_revision = 'SYSTEM'
|
|
|
442 if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
|
|
|
443 try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
|
|
|
444 # this ONLY happens at tool generation by an admin - the generated tool always uses the default of system so path is from local env.sh
|
|
|
445 packdetails = opts.envshpath.split(os.path.sep)[-4:-1] # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
|
|
|
446 self.interpreter_owner = packdetails[0]
|
|
|
447 self.interpreter_pack = packdetails[1]
|
|
|
448 self.interpreter_name = packdetails[1].split('_')[1].upper()
|
|
|
449 self.interpreter_revision = packdetails[2]
|
|
|
450 self.interpreter_version = '.'.join(packdetails[1].split('_')[2:])
|
|
|
451 except:
|
|
|
452 pass
|
|
|
453 self.outFormats = opts.output_format
|
|
|
454 self.inputFormats = opts.input_formats
|
|
|
455 self.test1Output = '%s_test1_output.xls' % self.toolname
|
|
|
456 self.test1HTML = '%s_test1_output.html' % self.toolname
|
|
|
457
|
|
|
458 def makeXML(self):
|
|
|
459 """
|
|
|
460 Create a Galaxy xml tool wrapper for the new script as a string to write out
|
|
|
461 fixme - use templating or something less fugly than this example of what we produce
|
|
|
462
|
|
|
463 <tool id="reverse" name="reverse" version="0.01">
|
|
|
464 <description>a tabular file</description>
|
|
|
465 <command interpreter="python">
|
|
|
466 reverse.py --script_path "$runMe" --interpreter "python"
|
|
|
467 --tool_name "reverse" --input_tab "$input1" --output_tab "$output1"
|
|
|
468 </command>
|
|
|
469 <inputs>
|
|
|
470 <param name="input1" type="data" format="tabular" label="Select one or more input files from your history"/>
|
|
|
471 <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
|
|
|
472 </inputs>
|
|
|
473 <outputs>
|
|
|
474 <data format="tabular" name="output1q" label="${job_name}"/>
|
|
|
475
|
|
|
476 </outputs>
|
|
|
477 <help>
|
|
|
478
|
|
|
479 **What it Does**
|
|
|
480
|
|
|
481 Reverse the columns in a tabular file
|
|
|
482
|
|
|
483 </help>
|
|
|
484 <configfiles>
|
|
|
485 <configfile name="runMe">
|
|
|
486
|
|
|
487 # reverse order of columns in a tabular file
|
|
|
488 import sys
|
|
|
489 inp = sys.argv[1]
|
|
|
490 outp = sys.argv[2]
|
|
|
491 i = open(inp,'r')
|
|
|
492 o = open(outp,'w')
|
|
|
493 for row in i:
|
|
|
494 rs = row.rstrip().split('\t')
|
|
|
495 rs.reverse()
|
|
|
496 o.write('\t'.join(rs))
|
|
|
497 o.write('\n')
|
|
|
498 i.close()
|
|
|
499 o.close()
|
|
|
500
|
|
|
501
|
|
|
502 </configfile>
|
|
|
503 </configfiles>
|
|
|
504 </tool>
|
|
|
505
|
|
|
506 """
|
|
|
507
|
|
|
508 # these templates need a dict with the right keys to match the parameters - outputs, help, code...
|
|
|
509
|
|
|
510 xdict = {}
|
|
|
511 xdict['additionalParams'] = ''
|
|
|
512 xdict['additionalInputs'] = ''
|
|
|
513 if self.opts.additional_parameters:
|
|
|
514 if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
|
|
|
515 xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % \
|
|
|
516 (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
|
|
|
517 xdict['additionalParams'] = '\n'.join(['<param name="%s" value="%s" />' % (x.split(',')[0],html_escape(x.split(',')[1])) for x in self.opts.additional_parameters])
|
|
|
518 xdict['interpreter_owner'] = self.interpreter_owner
|
|
|
519 xdict['interpreter_version'] = self.interpreter_version
|
|
|
520 xdict['interpreter_pack'] = self.interpreter_pack
|
|
|
521 xdict['interpreter_name'] = self.interpreter_name
|
|
|
522 xdict['requirements'] = ''
|
|
|
523 if self.opts.include_dependencies == "yes":
|
|
|
524 if self.opts.envshpath <> 'system':
|
|
|
525 xdict['requirements'] = self.protorequirements_interpreter % xdict
|
|
|
526 else:
|
|
|
527 xdict['requirements'] = self.protorequirements
|
|
|
528 xdict['tool_version'] = self.opts.tool_version
|
|
|
529 xdict['test1HTML'] = self.test1HTML
|
|
|
530 xdict['test1Output'] = self.test1Output
|
|
|
531 xdict['test1Inputs'] = self.test1Inputs
|
|
|
532 if self.opts.make_HTML and self.opts.output_tab:
|
|
|
533 xdict['tooltests'] = self.tooltestsBoth % xdict
|
|
|
534 elif self.opts.make_HTML:
|
|
|
535 xdict['tooltests'] = self.tooltestsHTMLOnly % xdict
|
|
|
536 else:
|
|
|
537 xdict['tooltests'] = self.tooltestsTabOnly % xdict
|
|
|
538 xdict['script'] = self.escapedScript
|
|
|
539 # configfile is least painful way to embed script to avoid external dependencies
|
|
|
540 # but requires escaping of <, > and $ to avoid Mako parsing
|
|
|
541 if self.opts.help_text:
|
|
|
542 helptext = open(self.opts.help_text,'r').readlines()
|
|
|
543 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
|
|
|
544 xdict['help'] = ''.join([x for x in helptext])
|
|
|
545 else:
|
|
|
546 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
|
|
|
547 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
|
|
|
548 coda.append('\n')
|
|
|
549 coda.append(self.indentedScript)
|
|
|
550 coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
|
|
|
551 coda.append('See %s for details of that project' % (toolFactoryURL))
|
|
|
552 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
|
|
|
553 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
|
|
|
554 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
|
|
|
555 if self.opts.tool_desc:
|
|
|
556 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
|
|
|
557 else:
|
|
|
558 xdict['tooldesc'] = ''
|
|
|
559 xdict['command_outputs'] = ''
|
|
|
560 xdict['outputs'] = ''
|
|
|
561 if self.opts.input_tab:
|
|
|
562 cins = ['\n',]
|
|
|
563 cins.append('--input_formats %s' % self.opts.input_formats)
|
|
|
564 cins.append('#for intab in $input1:')
|
|
|
565 cins.append('--input_tab "${intab},${intab.name}"')
|
|
|
566 cins.append('#end for\n')
|
|
|
567 xdict['command_inputs'] = '\n'.join(cins)
|
|
|
568 xdict['inputs'] = '''<param name="input_tab" multiple="true" type="data" format="%s" label="Select one or more %s input files from your history"
|
|
|
569 help="Multiple inputs may be selected assuming the script can deal with them..."/> \n''' % (self.inputFormats,self.inputFormats)
|
|
|
570 else:
|
|
|
571 xdict['command_inputs'] = '' # assume no input - eg a random data generator
|
|
|
572 xdict['inputs'] = ''
|
|
|
573 if (len(self.opts.additional_parameters) > 0):
|
|
|
574 cins = ['\n',]
|
|
|
575 for params in self.opts.additional_parameters:
|
|
|
576 psplit = params.split(',') # name,value...
|
|
|
577 psplit[3] = html_escape(psplit[3])
|
|
|
578 if self.opts.edit_additional_parameters:
|
|
|
579 psplit[1] = '$%s' % psplit[0] # replace with form value
|
|
|
580 else:
|
|
|
581 psplit[1] = html_escape(psplit[1]) # leave prespecified value
|
|
|
582 cins.append('--additional_parameters """%s"""' % ','.join(psplit))
|
|
|
583 xdict['command_inputs'] = '%s\n%s' % (xdict['command_inputs'],'\n'.join(cins))
|
|
|
584 xdict['inputs'] += '<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
|
|
|
585 xdict['toolname'] = self.toolname
|
|
|
586 xdict['toolid'] = self.toolid
|
|
|
587 xdict['interpreter'] = self.opts.interpreter
|
|
|
588 xdict['scriptname'] = self.sfile
|
|
|
589 if self.opts.make_HTML:
|
|
|
590 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
|
|
|
591 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
|
|
|
592 else:
|
|
|
593 xdict['command_outputs'] += ' --output_dir "./"'
|
|
|
594 if self.opts.output_tab:
|
|
|
595 xdict['command_outputs'] += ' --output_tab "$output1"'
|
|
|
596 xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats
|
|
|
597 xdict['command'] = self.newCommand % xdict
|
|
|
598 if self.opts.citations:
|
|
|
599 citationstext = open(self.opts.citations,'r').read()
|
|
|
600 citation_tuples = parse_citations(citationstext)
|
|
|
601 citations_xml = ""
|
|
|
602 for citation_type, citation_content in citation_tuples:
|
|
|
603 citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
|
|
|
604 citations_xml += citation_xml
|
|
|
605 xdict['citations'] = citations_xml
|
|
|
606 else:
|
|
|
607 xdict['citations'] = ""
|
|
|
608 xmls = self.newXML % xdict
|
|
|
609 xf = open(self.xmlfile,'w')
|
|
|
610 xf.write(xmls)
|
|
|
611 xf.write('\n')
|
|
|
612 xf.close()
|
|
|
613 # ready for the tarball
|
|
|
614
|
|
|
615
|
|
|
616 def makeTooltar(self):
|
|
|
617 """
|
|
|
618 a tool is a gz tarball with eg
|
|
|
619 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
620 """
|
|
|
621 retval = self.run()
|
|
|
622 if retval:
|
|
|
623 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
|
|
|
624 sys.exit(1)
|
|
|
625 tdir = self.toolname
|
|
|
626 os.mkdir(tdir)
|
|
|
627 self.makeXML()
|
|
|
628 if self.opts.help_text:
|
|
|
629 hlp = open(self.opts.help_text,'r').read()
|
|
|
630 else:
|
|
|
631 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
|
|
|
632 readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name,
|
|
|
633 'interpreter_owner':self.interpreter_owner,'interpreter_pack':self.interpreter_pack}
|
|
|
634 if self.opts.include_dependencies == "yes":
|
|
|
635 if self.opts.envshpath == 'system':
|
|
|
636 tooldepcontent = self.toolhtmldepskel % readme_dict
|
|
|
637 else:
|
|
|
638 tooldepcontent = self.toolhtmldepinterpskel % readme_dict
|
|
|
639 else:
|
|
|
640 tooldepcontent = self.emptytoolhtmldepskel % readme_dict
|
|
|
641 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
|
|
|
642 depf.write(tooldepcontent)
|
|
|
643 depf.write('\n')
|
|
|
644 depf.close()
|
|
|
645 testdir = os.path.join(tdir,'test-data')
|
|
|
646 os.mkdir(testdir) # make tests directory
|
|
|
647 for i,intab in enumerate(self.opts.input_tab):
|
|
|
648 si = self.opts.input_tab[i]
|
|
|
649 if si.find(',') <> -1:
|
|
|
650 s = si.split(',')[0]
|
|
|
651 si = s
|
|
|
652 dest = os.path.join(testdir,os.path.basename(si))
|
|
|
653 if si <> dest:
|
|
|
654 shutil.copyfile(si,dest)
|
|
|
655 if self.opts.output_tab:
|
|
|
656 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
|
|
|
657 if self.opts.make_HTML:
|
|
|
658 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
|
|
|
659 if self.opts.output_dir:
|
|
|
660 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
|
|
|
661 outpif = '%s.py' % self.toolname # new name
|
|
|
662 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
|
|
|
663 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
|
|
|
664 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
|
|
|
665 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
|
|
|
666 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
|
|
|
667 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
|
|
|
668 notes += pi
|
|
|
669 outpi = open(outpiname,'w')
|
|
|
670 outpi.write(''.join(notes))
|
|
|
671 outpi.write('\n')
|
|
|
672 outpi.close()
|
|
|
673 stname = os.path.join(tdir,self.sfile)
|
|
|
674 if not os.path.exists(stname):
|
|
|
675 shutil.copyfile(self.sfile, stname)
|
|
|
676 xtname = os.path.join(tdir,self.xmlfile)
|
|
|
677 if not os.path.exists(xtname):
|
|
|
678 shutil.copyfile(self.xmlfile,xtname)
|
|
|
679 tarpath = "%s.tar.gz" % self.toolname
|
|
|
680 tar = tarfile.open(tarpath, "w:gz")
|
|
|
681 tar.add(tdir,arcname='%s' % self.toolname)
|
|
|
682 tar.close()
|
|
|
683 shutil.copyfile(tarpath,self.opts.new_tool)
|
|
|
684 shutil.rmtree(tdir)
|
|
|
685 ## TODO: replace with optional direct upload to local toolshed?
|
|
|
686 return retval
|
|
|
687
|
|
|
688
|
|
|
689 def compressPDF(self,inpdf=None,thumbformat='png'):
|
|
|
690 """need absolute path to pdf
|
|
|
691 note that GS gets confoozled if no $TMP or $TEMP
|
|
|
692 so we set it
|
|
|
693 """
|
|
|
694 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
|
|
|
695 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
|
|
|
696 sto = open(hlog,'a')
|
|
|
697 our_env = os.environ.copy()
|
|
|
698 our_tmp = our_env.get('TMP',None)
|
|
|
699 if not our_tmp:
|
|
|
700 our_tmp = our_env.get('TEMP',None)
|
|
|
701 if not (our_tmp and os.path.exists(our_tmp)):
|
|
|
702 newtmp = os.path.join(self.opts.output_dir,'tmp')
|
|
|
703 try:
|
|
|
704 os.mkdir(newtmp)
|
|
|
705 except:
|
|
|
706 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
|
|
|
707 our_env['TEMP'] = newtmp
|
|
|
708 if not self.temp_warned:
|
|
|
709 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
|
|
|
710 self.temp_warned = True
|
|
|
711 outpdf = '%s_compressed' % inpdf
|
|
|
712 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
|
|
|
713 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
714 retval1 = x.wait()
|
|
|
715 sto.close()
|
|
|
716 if retval1 == 0:
|
|
|
717 os.unlink(inpdf)
|
|
|
718 shutil.move(outpdf,inpdf)
|
|
|
719 os.unlink(hlog)
|
|
|
720 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
|
|
|
721 sto = open(hlog,'w')
|
|
|
722 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
|
|
|
723 if self.useGM:
|
|
|
724 cl2 = ['gm', 'convert', inpdf, outpng]
|
|
|
725 else: # assume imagemagick
|
|
|
726 cl2 = ['convert', inpdf, outpng]
|
|
|
727 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
728 retval2 = x.wait()
|
|
|
729 sto.close()
|
|
|
730 if retval2 == 0:
|
|
|
731 os.unlink(hlog)
|
|
|
732 retval = retval1 or retval2
|
|
|
733 return retval
|
|
|
734
|
|
|
735
|
|
|
736 def getfSize(self,fpath,outpath):
|
|
|
737 """
|
|
|
738 format a nice file size string
|
|
|
739 """
|
|
|
740 size = ''
|
|
|
741 fp = os.path.join(outpath,fpath)
|
|
|
742 if os.path.isfile(fp):
|
|
|
743 size = '0 B'
|
|
|
744 n = float(os.path.getsize(fp))
|
|
|
745 if n > 2**20:
|
|
|
746 size = '%1.1f MB' % (n/2**20)
|
|
|
747 elif n > 2**10:
|
|
|
748 size = '%1.1f KB' % (n/2**10)
|
|
|
749 elif n > 0:
|
|
|
750 size = '%d B' % (int(n))
|
|
|
751 return size
|
|
|
752
|
|
|
753 def makeHtml(self):
|
|
|
754 """ Create an HTML file content to list all the artifacts found in the output_dir
|
|
|
755 """
|
|
|
756
|
|
|
757 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
|
758 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
|
759 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
|
760 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
|
|
|
761 <title></title>
|
|
|
762 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
|
|
763 </head>
|
|
|
764 <body>
|
|
|
765 <div class="toolFormBody">
|
|
|
766 """
|
|
|
767 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
|
|
|
768 galhtmlpostfix = """</div></body></html>\n"""
|
|
|
769
|
|
|
770 flist = os.listdir(self.opts.output_dir)
|
|
|
771 flist = [x for x in flist if x <> 'Rplots.pdf']
|
|
|
772 flist.sort()
|
|
|
773 html = []
|
|
|
774 html.append(galhtmlprefix % progname)
|
|
|
775 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
|
|
|
776 fhtml = []
|
|
|
777 if len(flist) > 0:
|
|
|
778 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
|
|
|
779 logfiles.sort()
|
|
|
780 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
|
|
|
781 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
|
|
|
782 pdflist = []
|
|
|
783 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
|
|
|
784 for rownum,fname in enumerate(flist):
|
|
|
785 dname,e = os.path.splitext(fname)
|
|
|
786 sfsize = self.getfSize(fname,self.opts.output_dir)
|
|
|
787 if e.lower() == '.pdf' : # compress and make a thumbnail
|
|
|
788 thumb = '%s.%s' % (dname,self.thumbformat)
|
|
|
789 pdff = os.path.join(self.opts.output_dir,fname)
|
|
|
790 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
|
|
|
791 if retval == 0:
|
|
|
792 pdflist.append((fname,thumb))
|
|
|
793 else:
|
|
|
794 pdflist.append((fname,fname))
|
|
|
795 if (rownum+1) % 2 == 0:
|
|
|
796 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
797 else:
|
|
|
798 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
799 for logfname in logfiles: # expect at least tlog - if more
|
|
|
800 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
|
|
|
801 sectionname = 'All tool run'
|
|
|
802 if (len(logfiles) > 1):
|
|
|
803 sectionname = 'Other'
|
|
|
804 ourpdfs = pdflist
|
|
|
805 else:
|
|
|
806 realname = os.path.basename(logfname)
|
|
|
807 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
|
|
|
808 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
|
|
|
809 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
|
|
|
810 nacross = 1
|
|
|
811 npdf = len(ourpdfs)
|
|
|
812
|
|
|
813 if npdf > 0:
|
|
|
814 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
|
|
|
815 if int(nacross)**2 != npdf:
|
|
|
816 nacross += 1
|
|
|
817 nacross = int(nacross)
|
|
|
818 width = min(400,int(1200/nacross))
|
|
|
819 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
|
|
|
820 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
|
|
|
821 ntogo = nacross # counter for table row padding with empty cells
|
|
|
822 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
|
|
|
823 for i,paths in enumerate(ourpdfs):
|
|
|
824 fname,thumb = paths
|
|
|
825 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
|
|
|
826 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
|
|
|
827 if ((i+1) % nacross == 0):
|
|
|
828 s += '</tr>\n'
|
|
|
829 ntogo = 0
|
|
|
830 if i < (npdf - 1): # more to come
|
|
|
831 s += '<tr>'
|
|
|
832 ntogo = nacross
|
|
|
833 else:
|
|
|
834 ntogo -= 1
|
|
|
835 html.append(s)
|
|
|
836 if html[-1].strip().endswith('</tr>'):
|
|
|
837 html.append('</table></div>\n')
|
|
|
838 else:
|
|
|
839 if ntogo > 0: # pad
|
|
|
840 html.append('<td> </td>'*ntogo)
|
|
|
841 html.append('</tr></table></div>\n')
|
|
|
842 logt = open(logfname,'r').readlines()
|
|
|
843 logtext = [x for x in logt if x.strip() > '']
|
|
|
844 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
|
|
|
845 if len(logtext) > 1:
|
|
|
846 html.append('\n<pre>\n')
|
|
|
847 html += logtext
|
|
|
848 html.append('\n</pre>\n')
|
|
|
849 else:
|
|
|
850 html.append('%s is empty<br/>' % logfname)
|
|
|
851 if len(fhtml) > 0:
|
|
|
852 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
|
|
|
853 fhtml.append('</table></div><br/>')
|
|
|
854 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
|
|
|
855 html += fhtml # add all non-pdf files to the end of the display
|
|
|
856 else:
|
|
|
857 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
|
|
|
858 html.append(galhtmlpostfix)
|
|
|
859 htmlf = file(self.opts.output_html,'w')
|
|
|
860 htmlf.write('\n'.join(html))
|
|
|
861 htmlf.write('\n')
|
|
|
862 htmlf.close()
|
|
|
863 self.html = html
|
|
|
864
|
|
|
865
|
|
|
866
|
|
|
867 def run(self):
|
|
|
868 """
|
|
|
869 Some devteam tools have this defensive stderr read so I'm keeping with the faith
|
|
|
870 Feel free to update.
|
|
|
871 """
|
|
|
872 if self.opts.envshpath <> 'system':
|
|
|
873 shell_source(self.opts.envshpath)
|
|
|
874 # this only happens at tool generation - the generated tool relies on the dependencies all being set up
|
|
|
875 # at toolshed installation by sourcing local env.sh
|
|
|
876 if self.opts.output_dir:
|
|
|
877 ste = open(self.elog,'wb')
|
|
|
878 sto = open(self.tlog,'wb')
|
|
|
879 s = ' '.join(self.cl)
|
|
|
880 sto.write('## Executing Toolfactory generated command line = %s\n' % s)
|
|
|
881 sto.flush()
|
|
|
882 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir)
|
|
|
883 retval = p.wait()
|
|
|
884 sto.close()
|
|
|
885 ste.close()
|
|
|
886 tmp_stderr = open( self.elog, 'rb' )
|
|
|
887 err = ''
|
|
|
888 buffsize = 1048576
|
|
|
889 try:
|
|
|
890 while True:
|
|
|
891 err += tmp_stderr.read( buffsize )
|
|
|
892 if not err or len( err ) % buffsize != 0:
|
|
|
893 break
|
|
|
894 except OverflowError:
|
|
|
895 pass
|
|
|
896 tmp_stderr.close()
|
|
|
897 else:
|
|
|
898 p = subprocess.Popen(self.cl,shell=False)
|
|
|
899 retval = p.wait()
|
|
|
900 if self.opts.output_dir:
|
|
|
901 if retval <> 0 and err: # problem
|
|
|
902 print >> sys.stderr,err
|
|
|
903 if self.opts.make_HTML:
|
|
|
904 self.makeHtml()
|
|
|
905 return retval
|
|
|
906
|
|
|
907
|
|
|
908
|
|
|
909 def main():
|
|
|
910 u = """
|
|
|
911 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
912 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
913 </command>
|
|
|
914 """
|
|
|
915 op = optparse.OptionParser()
|
|
|
916 a = op.add_option
|
|
|
917 a('--script_path',default=None)
|
|
|
918 a('--tool_name',default=None)
|
|
|
919 a('--interpreter',default=None)
|
|
|
920 a('--output_dir',default='./')
|
|
|
921 a('--output_html',default=None)
|
|
|
922 a('--input_tab',default=[], action="append") # these are "galaxypath,metadataname" pairs
|
|
|
923 a("--input_formats",default="tabular")
|
|
|
924 a('--output_tab',default=None)
|
|
|
925 a('--output_format',default='tabular')
|
|
|
926 a('--user_email',default='Unknown')
|
|
|
927 a('--bad_user',default=None)
|
|
|
928 a('--make_Tool',default=None)
|
|
|
929 a('--make_HTML',default=None)
|
|
|
930 a('--help_text',default=None)
|
|
|
931 a('--tool_desc',default=None)
|
|
|
932 a('--new_tool',default=None)
|
|
|
933 a('--tool_version',default=None)
|
|
|
934 a('--include_dependencies',default=None)
|
|
|
935 a('--citations',default=None)
|
|
|
936 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
|
|
|
937 a('--edit_additional_parameters', action="store_true", default=False)
|
|
|
938 a('--envshpath',default="system")
|
|
|
939 opts, args = op.parse_args()
|
|
|
940 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
|
|
|
941 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
|
|
|
942 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
|
|
|
943 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
|
|
|
944 if opts.output_dir:
|
|
|
945 try:
|
|
|
946 os.makedirs(opts.output_dir)
|
|
|
947 except:
|
|
|
948 pass
|
|
|
949 opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab]
|
|
|
950 for i,x in enumerate(opts.additional_parameters): # remove quotes we need to deal with spaces in CL params
|
|
|
951 opts.additional_parameters[i] = opts.additional_parameters[i].replace('"','')
|
|
|
952 r = ScriptRunner(opts)
|
|
|
953 if opts.make_Tool:
|
|
|
954 retcode = r.makeTooltar()
|
|
|
955 else:
|
|
|
956 retcode = r.run()
|
|
|
957 os.unlink(r.sfile)
|
|
|
958 if retcode:
|
|
|
959 sys.exit(retcode) # indicate failure to job runner
|
|
|
960
|
|
|
961
|
|
|
962 if __name__ == "__main__":
|
|
|
963 main()
|
|
|
964
|
|
|
965
|
|
|
966
|
