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30
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1 # rgToolFactory.py
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2 # see https://github.com/fubar2/toolfactory
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory
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9 #
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10 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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11 # Decided to
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12 # 1. Fix the toolfactory so it works - done for simplest case
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13 # 2. Fix planemo so the toolfactory function works
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14 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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15 #
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16 # removed all the old complications including making the new tool use this same script
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17 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
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18 # No support for automatic HTML file creation from arbitrary outputs
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19 # TODO: add option to run that code as a post execution hook
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20 # TODO: add additional history input parameters - currently only one
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21
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22 import sys
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23 import subprocess
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24 import shutil
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25 import os
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26 import time
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27 import tempfile
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28 import argparse
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29 import tarfile
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30 import re
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31 import galaxyxml.tool as gxt
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32 import galaxyxml.tool.parameters as gxtp
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33 import logging
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34
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35
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36 progname = os.path.split(sys.argv[0])[1]
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37 myversion = 'V2.1 July 2020'
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38 verbose = True
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39 debug = True
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40 toolFactoryURL = 'https://github.com/fubar2/toolfactory'
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41 ourdelim = '~~~'
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42
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43 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help"
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44 IPATHPOS = 0
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45 ICLPOS = 1
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46 IFMTPOS = 2
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47 ILABPOS = 3
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48 IHELPOS = 4
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49 IOCLPOS = 5
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50 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL
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51 ONAMEPOS = 0
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52 OFMTPOS = 1
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53 OCLPOS = 2
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54 OOCLPOS = 3
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55
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56 #--additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL"
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57 ANAMEPOS = 0
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58 AVALPOS = 1
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59 ALABPOS = 2
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60 AHELPPOS = 3
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61 ATYPEPOS = 4
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62 ACLPOS = 5
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63 AOCLPOS = 6
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64
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65 def timenow():
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66 """return current time as a string
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67 """
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68 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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69
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70
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71 def quote_non_numeric(s):
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72 """return a prequoted string for non-numerics
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73 useful for perl and Rscript parameter passing?
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74 """
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75 try:
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76 _ = float(s)
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77 return s
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78 except ValueError:
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79 return '"%s"' % s
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80
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81
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82 html_escape_table = {
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83 "&": "&",
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84 ">": ">",
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85 "<": "<",
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86 "$": r"\$"
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87 }
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88
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89
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90 def html_escape(text):
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91 """Produce entities within text."""
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92 return "".join(html_escape_table.get(c, c) for c in text)
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93
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94
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95 def html_unescape(text):
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96 """Revert entities within text. Multiple character targets so use replace"""
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97 t = text.replace('&', '&')
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98 t = t.replace('>', '>')
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99 t = t.replace('<', '<')
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100 t = t.replace('\\$', '$')
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101 return t
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102
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103
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104 def parse_citations(citations_text):
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105 """
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106 """
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107 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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108 citation_tuples = []
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109 for citation in citations:
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110 if citation.startswith("doi"):
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111 citation_tuples.append(("doi", citation[len("doi"):].strip()))
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112 else:
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113 citation_tuples.append(
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114 ("bibtex", citation[len("bibtex"):].strip()))
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115 return citation_tuples
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116
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117
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118 class ScriptRunner:
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119 """Wrapper for an arbitrary script
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120 uses galaxyxml
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121
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122 """
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123
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124
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125 def __init__(self, args=None):
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126 """
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127 prepare command line cl for running the tool here
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128 and prepare elements needed for galaxyxml tool generation
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129 """
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130
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131 self.infiles = [x.split(ourdelim) for x in args.input_files]
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132 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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133 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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134 self.args = args
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135 self.cleanuppar()
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136 self.lastclredirect = None
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137 self.lastxclredirect = None
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138 self.cl = []
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139 self.xmlcl = []
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140 aCL = self.cl.append
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141 assert args.parampass in ['0','argparse','positional'],'Parameter passing in args.parampass must be "0","positional" or "argparse"'
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142 self.tool_name = re.sub('[^a-zA-Z0-9_]+', '', args.tool_name)
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143 self.tool_id = self.tool_name
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144 self.xmlfile = '%s.xml' % self.tool_name
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145 if self.args.runmode == "Executable" or self.args.runmode == "system": # binary - no need
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146 aCL(self.args.exe_package) # this little CL will just run
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147 else:
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148 rx = open(self.args.script_path, 'r').readlines()
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149 rx = [x.rstrip() for x in rx ]
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150 rxcheck = [x.strip() for x in rx if x.strip() > '']
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151 assert len(rxcheck) > 0,"Supplied script is empty. Cannot run"
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152 self.script = '\n'.join(rx)
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153 fhandle, self.sfile = tempfile.mkstemp(
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154 prefix=self.tool_name, suffix=".%s" % (args.interpreter_name))
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155 tscript = open(self.sfile, 'w')
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156 tscript.write(self.script)
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157 tscript.close()
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158 self.indentedScript = " %s" % '\n'.join(
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159 [' %s' % html_escape(x) for x in rx])
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160 self.escapedScript = "%s" % '\n'.join(
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161 [' %s' % html_escape(x) for x in rx])
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162 art = '%s.%s' % (self.tool_name, args.interpreter_name)
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163 artifact = open(art, 'wb')
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164 artifact.write(bytes(self.script, "utf8"))
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165 artifact.close()
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166 aCL(self.args.interpreter_name)
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167 aCL(self.sfile)
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168 self.elog = "%s_error_log.txt" % self.tool_name
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169 self.tlog = "%s_runner_log.txt" % self.tool_name
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170
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171 if self.args.parampass == '0':
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172 self.clsimple()
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173 else:
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174 clsuffix = []
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175 xclsuffix = []
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176 for i, p in enumerate(self.infiles):
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177 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS]]
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178 clsuffix.append(appendme)
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179 xclsuffix.append([p[IOCLPOS],p[ICLPOS],'$%s' % p[ICLPOS]])
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180 #print('##infile i=%d, appendme=%s' % (i,appendme))
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181 for i, p in enumerate(self.outfiles):
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182 if p[OOCLPOS] == "STDOUT":
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183 self.lastclredirect = ['>',p[ONAMEPOS]]
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184 self.lastxclredirect = ['>','$%s' % p[OCLPOS]]
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185 #print('##outfiles i=%d lastclredirect = %s' % (i,self.lastclredirect))
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186 else:
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187 appendme = [p[OOCLPOS], p[OCLPOS],p[ONAMEPOS]]
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188 clsuffix.append(appendme)
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189 xclsuffix.append([p[OOCLPOS], p[OCLPOS],'$%s' % p[ONAMEPOS]])
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190 #print('##outfiles i=%d' % i,'appendme',appendme)
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191 for p in self.addpar:
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192 appendme = [p[AOCLPOS], p[ACLPOS], p[AVALPOS]]
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193 clsuffix.append(appendme)
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194 xclsuffix.append([p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS]])
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195 #print('##adpar %d' % i,'appendme=',appendme)
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196 clsuffix.sort()
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197 xclsuffix.sort()
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198 self.xclsuffix = xclsuffix
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199 self.clsuffix = clsuffix
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200 if self.args.parampass == 'positional':
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201 self.clpositional()
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202 else:
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203 self.clargparse()
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204
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205 def cleanuppar(self):
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206 """ positional parameters are complicated by their numeric ordinal"""
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207 for i,p in enumerate(self.infiles):
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208 if self.args.parampass == 'positional':
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209 assert p[ICLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[ICLPOS],p[ILABPOS])
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210 p.append(p[ICLPOS])
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211 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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212 scl = 'input%d' % (i+1)
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213 p[ICLPOS] = scl
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214 self.infiles[i] = p
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215 for i,p in enumerate(self.outfiles): # trying to automagically gather using extensions
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216 if self.args.parampass == 'positional' and p[OCLPOS] != "STDOUT":
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217 assert p[OCLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[OCLPOS],p[ONAMEPOS])
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218 p.append(p[OCLPOS])
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219 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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220 scl = p[ONAMEPOS]
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221 p[OCLPOS] = scl
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222 self.outfiles[i] = p
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223 for i,p in enumerate(self.addpar):
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224 if self.args.parampass == 'positional':
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225 assert p[ACLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[ACLPOS],p[ANAMEPOS])
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226 p.append(p[ACLPOS])
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227 if p[ACLPOS].isdigit():
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228 scl = 'input%s' % p[ACLPOS]
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229 p[ACLPOS] = scl
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230 self.addpar[i] = p
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231
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232
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233
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234 def clsimple(self):
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235 """ no parameters - uses < and > for i/o
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236 """
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237 aCL = self.cl.append
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238 aCL('<')
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239 aCL(self.infiles[0][IPATHPOS])
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240 aCL('>')
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241 aCL(self.outfiles[0][OCLPOS])
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242 aXCL = self.xmlcl.append
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243 aXCL('<')
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244 aXCL('$%s' % self.infiles[0][ICLPOS])
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245 aXCL('>')
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246 aXCL('$%s' % self.outfiles[0][ONAMEPOS])
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247
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248
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249 def clpositional(self):
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250 # inputs in order then params
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251 aCL = self.cl.append
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252 for (o_v,k, v) in self.clsuffix:
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253 if " " in v:
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254 aCL("%s" % v)
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255 else:
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256 aCL(v)
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257 aXCL = self.xmlcl.append
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258 for (o_v,k, v) in self.xclsuffix:
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259 aXCL(v)
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260 if self.lastxclredirect:
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261 aXCL(self.lastxclredirect[0])
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262 aXCL(self.lastxclredirect[1])
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263
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264
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265
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266 def clargparse(self):
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267 """ argparse style
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268 """
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269 aCL = self.cl.append
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270 aXCL = self.xmlcl.append
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271 # inputs then params in argparse named form
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272 for (o_v,k, v) in self.xclsuffix:
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273 aXCL(k)
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274 aXCL(v)
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275 for (o_v,k, v) in self.clsuffix:
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276 if len(k.strip()) == 1:
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277 k = '-%s' % k
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278 else:
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279 k = '--%s' % k
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280 aCL(k)
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281 aCL(v)
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282
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283
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284
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285
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286 def makeXML(self):
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287 """
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288 Create a Galaxy xml tool wrapper for the new script
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289 Uses galaxyhtml
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290 Hmmm. How to get the command line into correct order...
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291 """
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292
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293 if self.args.interpreter_name:
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294 exe = "$runMe"
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295 interp = self.args.interpreter_name
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296 else:
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297 interp = None
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298 exe = self.args.exe_package
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299 assert exe is not None, 'No interpeter or executable passed in to makeXML'
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300 tool = gxt.Tool(self.args.tool_name, self.tool_id,
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301 self.args.tool_version, self.args.tool_desc, exe)
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302 tool.command_line_override = self.xmlcl
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303 print('#### tool cl override=',self.xmlcl)
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304 if interp:
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305 tool.interpreter = interp
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306 if self.args.help_text:
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307 helptext = open(self.args.help_text, 'r').readlines()
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308 helptext = [html_escape(x) for x in helptext]
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309 tool.help = ''.join([x for x in helptext])
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310 else:
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311 tool.help = 'Please ask the tool author (%s) for help \
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312 as none was supplied at tool generation\n' % (self.args.user_email)
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313 tool.version_command = None # do not want
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314 tinputs = gxtp.Inputs()
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315 toutputs = gxtp.Outputs()
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316 requirements = gxtp.Requirements()
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317 testparam = []
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318 is_positional = (self.args.parampass == 'positional')
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319 if self.args.interpreter_name:
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320 if self.args.interpreter_name == 'python':
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321 requirements.append(gxtp.Requirement(
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322 'package', 'python', self.args.interpreter_version))
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323 elif self.args.interpreter_name not in ['bash', 'sh']:
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324 requirements.append(gxtp.Requirement(
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325 'package', self.args.interpreter_name, self.args.interpreter_version))
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326 else:
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327 if self.args.exe_package and self.args.parampass != "system":
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328 requirements.append(gxtp.Requirement(
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329 'package', self.args.exe_package, self.args.exe_package_version))
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330 tool.requirements = requirements
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331 if self.args.parampass == '0':
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332 alab = self.infiles[0][ILABPOS]
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333 if len(alab) == 0:
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334 alab = self.infiles[0][ICLPOS]
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335 max1s = 'Maximum one input if parampass is 0 - more than one input files supplied - %s' % str(self.infiles)
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336 assert len(self.infiles) == 1,max1s
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337 newname = self.infiles[0][ICLPOS]
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338 aninput = gxtp.DataParam(newname, optional=False, label=alab, help=self.infiles[0][IHELPOS],
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339 format=self.infiles[0][IFMTPOS], multiple=False, num_dashes=0)
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340 aninput.command_line_override = '< $%s' % newname
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341 aninput.positional = is_positional
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342 tinputs.append(aninput)
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343 tp = gxtp.TestParam(name=newname, value='%s_sample' % newname)
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344 testparam.append(tp)
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345 newname = self.outfiles[0][OCLPOS]
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346 newfmt = self.outfiles[0][OFMTPOS]
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347 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
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348 anout.command_line_override = '> $%s' % newname
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349 anout.positional = is_positional
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350 toutputs.append(anout)
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351 tp = gxtp.TestOutput(name=newname, value='%s_sample' % newname,format=newfmt)
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352 testparam.append(tp)
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353 else:
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354 for p in self.outfiles:
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355 newname,newfmt,newcl,oldcl = p
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356 if is_positional:
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357 ndash = 0
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358 else:
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359 ndash = 2
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360 if len(newcl) < 2:
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361 ndash = 1
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362 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
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363 aparm.positional = is_positional
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364 if is_positional:
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365 if oldcl == "STDOUT":
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366 aparm.positional = 9999999
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367 aparm.command_line_override = "> $%s" % newcl
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368 else:
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369 aparm.positional = int(oldcl)
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370 aparm.command_line_override = '$%s' % newcl
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371 toutputs.append(aparm)
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372 tp = gxtp.TestOutput(name=newcl, value='%s_sample' % newcl ,format=newfmt)
|
|
|
373 testparam.append(tp)
|
|
|
374 for p in self.infiles:
|
|
|
375 newname = p[ICLPOS]
|
|
|
376 newfmt = p[IFMTPOS]
|
|
|
377 if is_positional:
|
|
|
378 ndash = 0
|
|
|
379 else:
|
|
|
380 if len(newname) > 1:
|
|
|
381 ndash = 2
|
|
|
382 else:
|
|
|
383 ndash = 1
|
|
|
384 if not len(p[ILABPOS]) > 0:
|
|
|
385 alab = p[ICLPOS]
|
|
|
386 else:
|
|
|
387 alab = p[ILABPOS]
|
|
|
388 aninput = gxtp.DataParam(newname, optional=False, label=alab, help=p[IHELPOS],
|
|
|
389 format=newfmt, multiple=False, num_dashes=ndash)
|
|
|
390 aninput.positional = is_positional
|
|
|
391 if is_positional:
|
|
|
392 aninput.positional = is_positional
|
|
|
393 tinputs.append(aninput)
|
|
|
394 tparm = gxtp.TestParam(name=newname, value='%s_sample' % newname )
|
|
|
395 testparam.append(tparm)
|
|
|
396 for p in self.addpar:
|
|
|
397 newname, newval, newlabel, newhelp, newtype, newcl, oldcl = p
|
|
|
398 if not len(newlabel) > 0:
|
|
|
399 newlabel = newname
|
|
|
400 if is_positional:
|
|
|
401 ndash = 0
|
|
|
402 else:
|
|
|
403 if len(newname) > 1:
|
|
|
404 ndash = 2
|
|
|
405 else:
|
|
|
406 ndash = 1
|
|
|
407 if newtype == "text":
|
|
|
408 aparm = gxtp.TextParam(
|
|
|
409 newname, label=newlabel, help=newhelp, value=newval, num_dashes=ndash)
|
|
|
410 elif newtype == "integer":
|
|
|
411 aparm = gxtp.IntegerParam(
|
|
|
412 newname, label=newname, help=newhelp, value=newval, num_dashes=ndash)
|
|
|
413 elif newtype == "float":
|
|
|
414 aparm = gxtp.FloatParam(
|
|
|
415 newname, label=newname, help=newhelp, value=newval, num_dashes=ndash)
|
|
|
416 else:
|
|
|
417 raise ValueError('Unrecognised parameter type "%s" for\
|
|
|
418 additional parameter %s in makeXML' % (newtype, newname))
|
|
|
419 aparm.positional = is_positional
|
|
|
420 if is_positional:
|
|
|
421 aninput.positional = int(oldcl)
|
|
|
422 tinputs.append(aparm)
|
|
|
423 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
424 testparam.append(tparm)
|
|
|
425 tool.outputs = toutputs
|
|
|
426 tool.inputs = tinputs
|
|
|
427 if not self.args.runmode in ['Executable','system']:
|
|
|
428 configfiles = gxtp.Configfiles()
|
|
|
429 configfiles.append(gxtp.Configfile(name="runMe", text=self.script))
|
|
|
430 tool.configfiles = configfiles
|
|
|
431 tests = gxtp.Tests()
|
|
|
432 test_a = gxtp.Test()
|
|
|
433 for tp in testparam:
|
|
|
434 test_a.append(tp)
|
|
|
435 tests.append(test_a)
|
|
|
436 tool.tests = tests
|
|
|
437 tool.add_comment('Created by %s at %s using the Galaxy Tool Factory.' % (
|
|
|
438 self.args.user_email, timenow()))
|
|
|
439 tool.add_comment('Source in git at: %s' % (toolFactoryURL))
|
|
|
440 tool.add_comment(
|
|
|
441 'Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573')
|
|
|
442 exml = tool.export()
|
|
|
443 xf = open(self.xmlfile, 'w')
|
|
|
444 xf.write(exml)
|
|
|
445 xf.write('\n')
|
|
|
446 xf.close()
|
|
|
447 # ready for the tarball
|
|
|
448
|
|
|
449 def makeTooltar(self):
|
|
|
450 """
|
|
|
451 a tool is a gz tarball with eg
|
|
|
452 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
453 NOTE names for test inputs and outputs are munged here so must
|
|
|
454 correspond to actual input and output names used on the generated cl
|
|
|
455 """
|
|
|
456 retval = self.run()
|
|
|
457 if retval:
|
|
|
458 sys.stderr.write(
|
|
|
459 '## Run failed. Cannot build yet. Please fix and retry')
|
|
|
460 sys.exit(1)
|
|
|
461 tdir = 'tfout'
|
|
|
462 if not os.path.exists(tdir):
|
|
|
463 os.mkdir(tdir)
|
|
|
464 self.makeXML()
|
|
|
465 testdir = os.path.join(tdir,'test-data')
|
|
|
466 if not os.path.exists(testdir):
|
|
|
467 os.mkdir(testdir) # make tests directory
|
|
|
468 for p in self.infiles:
|
|
|
469 pth = p[IPATHPOS]
|
|
|
470 dest = os.path.join(testdir, '%s_sample' %
|
|
|
471 p[ICLPOS])
|
|
|
472 shutil.copyfile(pth, dest)
|
|
|
473 for p in self.outfiles:
|
|
|
474 pth = p[OCLPOS]
|
|
|
475 if p[OOCLPOS] == 'STDOUT' or self.args.parampass == "0":
|
|
|
476 pth = p[ONAMEPOS]
|
|
|
477 dest = os.path.join(testdir,'%s_sample' % p[ONAMEPOS])
|
|
|
478 shutil.copyfile(pth, dest)
|
|
|
479 dest = os.path.join(tdir, p[ONAMEPOS])
|
|
|
480 shutil.copyfile(pth, dest)
|
|
|
481 else:
|
|
|
482 pth = p[OCLPOS]
|
|
|
483 dest = os.path.join(testdir,'%s_sample' % p[OCLPOS])
|
|
|
484 shutil.copyfile(pth, dest)
|
|
|
485 dest = os.path.join(tdir, p[OCLPOS])
|
|
|
486 shutil.copyfile(pth, dest)
|
|
|
487
|
|
|
488 if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
|
|
|
489 shutil.copyfile(self.tlog, os.path.join(
|
|
|
490 testdir, 'test1_log.txt'))
|
|
|
491 if not self.args.runmode in ['Executable','system']:
|
|
|
492 stname = os.path.join(tdir, '%s' % (self.sfile))
|
|
|
493 if not os.path.exists(stname):
|
|
|
494 shutil.copyfile(self.sfile, stname)
|
|
|
495 xtname = os.path.join(tdir,self.xmlfile)
|
|
|
496 if not os.path.exists(xtname):
|
|
|
497 shutil.copyfile(self.xmlfile, xtname)
|
|
|
498 tarpath = 'toolfactory_%s.tgz' % self.tool_name
|
|
|
499 tf = tarfile.open(tarpath,"w:gz")
|
|
|
500 tf.add(name=tdir,arcname=self.tool_name)
|
|
|
501 tf.close()
|
|
|
502 shutil.copyfile(tarpath, self.args.new_tool)
|
|
|
503 return retval
|
|
|
504
|
|
|
505 def run(self):
|
|
|
506 """
|
|
|
507 Some devteam tools have this defensive stderr read so I'm keeping with the faith
|
|
|
508 Feel free to update.
|
|
|
509 """
|
|
|
510 s = 'run cl=%s' % str(self.cl)
|
|
|
511
|
|
|
512 logging.debug(s)
|
|
|
513 scl = ' '.join(self.cl)
|
|
|
514 err = None
|
|
|
515 if self.args.parampass != '0':
|
|
|
516 ste = open(self.elog, 'wb')
|
|
|
517 if self.lastclredirect:
|
|
|
518 sto = open(self.lastclredirect[1],'wb') # is name of an output file
|
|
|
519 else:
|
|
|
520 sto = open(self.tlog, 'wb')
|
|
|
521 sto.write(
|
|
|
522 bytes('## Executing Toolfactory generated command line = %s\n' % scl, "utf8"))
|
|
|
523 sto.flush()
|
|
|
524 p = subprocess.run(self.cl, shell=False, stdout=sto,
|
|
|
525 stderr=ste)
|
|
|
526 sto.close()
|
|
|
527 ste.close()
|
|
|
528 tmp_stderr = open(self.elog, 'rb')
|
|
|
529 err = ''
|
|
|
530 buffsize = 1048576
|
|
|
531 try:
|
|
|
532 while True:
|
|
|
533 err += str(tmp_stderr.read(buffsize))
|
|
|
534 if not err or len(err) % buffsize != 0:
|
|
|
535 break
|
|
|
536 except OverflowError:
|
|
|
537 pass
|
|
|
538 tmp_stderr.close()
|
|
|
539 retval = p.returncode
|
|
|
540 else: # work around special case of simple scripts that take stdin and write to stdout
|
|
|
541 sti = open(self.infiles[0][IPATHPOS], 'rb')
|
|
|
542 sto = open(self.outfiles[0][ONAMEPOS], 'wb')
|
|
|
543 # must use shell to redirect
|
|
|
544 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
|
|
|
545 retval = p.returncode
|
|
|
546 sto.close()
|
|
|
547 sti.close()
|
|
|
548 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
|
|
|
549 os.unlink(self.tlog)
|
|
|
550 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
|
|
|
551 os.unlink(self.elog)
|
|
|
552 if p.returncode != 0 and err: # problem
|
|
|
553 sys.stderr.write(err)
|
|
|
554 logging.debug('run done')
|
|
|
555 return retval
|
|
|
556
|
|
|
557
|
|
|
558 def main():
|
|
|
559 """
|
|
|
560 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
561 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
562 </command>
|
|
|
563 """
|
|
|
564 parser = argparse.ArgumentParser()
|
|
|
565 a = parser.add_argument
|
|
|
566 a('--script_path', default='')
|
|
|
567 a('--tool_name', default=None)
|
|
|
568 a('--interpreter_name', default=None)
|
|
|
569 a('--interpreter_version', default=None)
|
|
|
570 a('--exe_package', default=None)
|
|
|
571 a('--exe_package_version', default=None)
|
|
|
572 a('--input_files', default=[], action="append")
|
|
|
573 a('--output_files', default=[], action="append")
|
|
|
574 a('--user_email', default='Unknown')
|
|
|
575 a('--bad_user', default=None)
|
|
|
576 a('--make_Tool', default=None)
|
|
|
577 a('--help_text', default=None)
|
|
|
578 a('--tool_desc', default=None)
|
|
|
579 a('--tool_version', default=None)
|
|
|
580 a('--citations', default=None)
|
|
|
581 a('--additional_parameters', action='append', default=[])
|
|
|
582 a('--edit_additional_parameters', action="store_true", default=False)
|
|
|
583 a('--parampass', default="positional")
|
|
|
584 a('--tfout', default="./tfout")
|
|
|
585 a('--new_tool',default="new_tool")
|
|
|
586 a('--runmode',default=None)
|
|
|
587 args = parser.parse_args()
|
|
|
588 assert not args.bad_user, 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' % (
|
|
|
589 args.bad_user, args.bad_user)
|
|
|
590 assert args.tool_name, '## Tool Factory expects a tool name - eg --tool_name=DESeq'
|
|
|
591 assert (args.interpreter_name or args.exe_package), '## Tool Factory wrapper expects an interpreter - eg --interpreter_name=Rscript or an executable package findable by the dependency management package'
|
|
|
592 assert args.exe_package or (len(args.script_path) > 0 and os.path.isfile(
|
|
|
593 args.script_path)), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable'
|
|
|
594 args.input_files = [x.replace('"', '').replace("'", '')
|
|
|
595 for x in args.input_files]
|
|
|
596 # remove quotes we need to deal with spaces in CL params
|
|
|
597 for i, x in enumerate(args.additional_parameters):
|
|
|
598 args.additional_parameters[i] = args.additional_parameters[i].replace(
|
|
|
599 '"', '')
|
|
|
600 r = ScriptRunner(args)
|
|
|
601 if args.make_Tool:
|
|
|
602 retcode = r.makeTooltar()
|
|
|
603 else:
|
|
|
604 retcode = r.run()
|
|
|
605 if retcode:
|
|
|
606 sys.exit(retcode) # indicate failure to job runner
|
|
|
607
|
|
|
608
|
|
|
609 if __name__ == "__main__":
|
|
|
610 main()
|
