annotate toolfactory/rgToolFactory2.py @ 62:881bd8c81ac9 draft

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author fubar
date Mon, 26 Oct 2020 02:51:54 +0000
parents d21517a36db8
children b3254219d4fb
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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
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9 # https://github.com/fubar2/toolfactory
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10 #
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11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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12 # Decided to
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13 # 1. Fix the toolfactory so it works - done for simplest case
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14 # 2. Fix planemo so the toolfactory function works
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15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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16 #
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17 # removed all the old complications including making the new tool use this same script
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18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
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19 # No support for automatic HTML file creation from arbitrary outputs
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20 # essential problem is to create two command lines - one for the tool xml and a different
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21 # one to run the executable with the supplied test data and settings
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22 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
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23
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24
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25 import argparse
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26 import logging
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27 import os
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28 import re
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29 import shutil
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30 import subprocess
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31 import sys
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32 import tarfile
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33 import tempfile
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34 import time
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35
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36 import galaxyxml.tool as gxt
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37 import galaxyxml.tool.parameters as gxtp
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38
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39 import lxml
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40
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41 import yaml
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42
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43 myversion = "V2.1 July 2020"
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44 verbose = True
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45 debug = True
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46 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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47 ourdelim = "~~~"
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48 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
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49 STDIOXML = """<stdio>
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50 <exit_code range="100:" level="debug" description="shite happens" />
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51 </stdio>"""
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52
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53 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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54 # ~~~$input_help"
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55 IPATHPOS = 0
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56 ICLPOS = 1
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57 IFMTPOS = 2
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58 ILABPOS = 3
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59 IHELPOS = 4
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60 IOCLPOS = 5
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61
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62 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
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63 ONAMEPOS = 0
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64 OFMTPOS = 1
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65 OCLPOS = 2
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66 OTESTPOS = 3
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67 OOCLPOS = 4
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70 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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71 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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72 ANAMEPOS = 0
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73 AVALPOS = 1
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74 ALABPOS = 2
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75 AHELPPOS = 3
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76 ATYPEPOS = 4
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77 ACLPOS = 5
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78 AOVERPOS = 6
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79 AOCLPOS = 7
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82 foo = len(lxml.__version__)
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83 # fug you, flake8. Say my name!
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84 FAKEEXE = "~~~REMOVE~~~ME~~~"
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85 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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86 # with override.
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89 def timenow():
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90 """return current time as a string
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91 """
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92 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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93
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95 def quote_non_numeric(s):
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96 """return a prequoted string for non-numerics
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97 useful for perl and Rscript parameter passing?
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98 """
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99 try:
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100 _ = float(s)
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101 return s
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102 except ValueError:
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103 return '"%s"' % s
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105
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106 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
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107
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108
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109 def html_escape(text):
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110 """Produce entities within text."""
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111 return "".join(html_escape_table.get(c, c) for c in text)
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112
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113
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114 def html_unescape(text):
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115 """Revert entities within text. Multiple character targets so use replace"""
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116 t = text.replace("&amp;", "&")
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117 t = t.replace("&gt;", ">")
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118 t = t.replace("&lt;", "<")
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119 t = t.replace("\\$", "$")
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120 return t
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121
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122
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123 def parse_citations(citations_text):
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124 """
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125 """
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126 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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127 citation_tuples = []
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128 for citation in citations:
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129 if citation.startswith("doi"):
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130 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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131 else:
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132 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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133 return citation_tuples
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134
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135
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136 class ScriptRunner:
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137 """Wrapper for an arbitrary script
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138 uses galaxyxml
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139
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140 """
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141
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142 def __init__(self, args=None):
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143 """
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144 prepare command line cl for running the tool here
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145 and prepare elements needed for galaxyxml tool generation
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146 """
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147 self.infiles = [x.split(ourdelim) for x in args.input_files]
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148 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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149 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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150 self.args = args
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151 self.cleanuppar()
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152 self.lastclredirect = None
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153 self.lastxclredirect = None
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154 self.cl = []
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155 self.xmlcl = []
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156 self.is_positional = self.args.parampass == "positional"
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157 if self.args.packages:
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158 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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159 else:
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160 self.executeme = self.args.sysexe
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161 assert (
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162 self.executeme is not None
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163 ), "No system or managed executable passed in. Cannot build"
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164 aCL = self.cl.append
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165 aXCL = self.xmlcl.append
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166 assert args.parampass in [
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167 "0",
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168 "argparse",
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169 "positional",
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170 ], 'args.parampass must be "0","positional" or "argparse"'
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171 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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172 self.tool_id = self.tool_name
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173 self.newtool = gxt.Tool(
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174 self.args.tool_name,
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175 self.tool_id,
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176 self.args.tool_version,
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177 self.args.tool_desc,
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178 FAKEEXE,
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179 )
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180 self.tooloutdir = "tfout"
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181 self.repdir = "TF_run_report_tempdir"
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182 self.testdir = os.path.join(self.tooloutdir, "test-data")
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183 if not os.path.exists(self.tooloutdir):
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184 os.mkdir(self.tooloutdir)
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185 if not os.path.exists(self.testdir):
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186 os.mkdir(self.testdir) # make tests directory
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187 if not os.path.exists(self.repdir):
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188 os.mkdir(self.repdir)
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189 self.tinputs = gxtp.Inputs()
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190 self.toutputs = gxtp.Outputs()
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191 self.testparam = []
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192 if self.args.script_path:
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193 self.prepScript()
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194 if self.args.command_override:
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195 scos = open(self.args.command_override, "r").readlines()
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196 self.command_override = [x.rstrip() for x in scos]
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197 else:
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198 self.command_override = None
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199 if self.args.test_override:
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200 stos = open(self.args.test_override, "r").readlines()
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diff changeset
201 self.test_override = [x.rstrip() for x in stos]
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diff changeset
202 else:
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diff changeset
203 self.test_override = None
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diff changeset
204 if self.args.cl_prefix: # DIY CL start
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diff changeset
205 clp = self.args.cl_prefix.split(" ")
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206 for c in clp:
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diff changeset
207 aCL(c)
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diff changeset
208 aXCL(c)
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209 else:
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diff changeset
210 if self.args.script_path:
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211 aCL(self.executeme)
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212 aCL(self.sfile)
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diff changeset
213 aXCL(self.executeme)
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214 aXCL("$runme")
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215 else:
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216 aCL(self.executeme) # this little CL will just run
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217 aXCL(self.executeme)
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diff changeset
218 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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diff changeset
219 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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220
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221 if self.args.parampass == "0":
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222 self.clsimple()
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223 else:
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224 clsuffix = []
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parents:
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225 xclsuffix = []
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226 for i, p in enumerate(self.infiles):
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227 if p[IOCLPOS] == "STDIN":
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228 appendme = [
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parents:
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229 p[IOCLPOS],
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parents:
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230 p[ICLPOS],
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parents:
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231 p[IPATHPOS],
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parents:
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232 "< %s" % p[IPATHPOS],
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233 ]
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parents:
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234 xappendme = [
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parents:
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235 p[IOCLPOS],
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parents:
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236 p[ICLPOS],
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parents:
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237 p[IPATHPOS],
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parents:
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238 "< $%s" % p[ICLPOS],
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parents:
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239 ]
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240 else:
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241 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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parents:
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242 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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243 clsuffix.append(appendme)
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244 xclsuffix.append(xappendme)
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245 for i, p in enumerate(self.outfiles):
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246 if p[OOCLPOS] == "STDOUT":
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247 self.lastclredirect = [">", p[ONAMEPOS]]
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parents:
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248 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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249 else:
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parents:
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250 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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251 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
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252 for p in self.addpar:
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diff changeset
253 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
48
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254 xclsuffix.append(
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255 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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256 )
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parents:
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257 clsuffix.sort()
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258 xclsuffix.sort()
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259 self.xclsuffix = xclsuffix
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260 self.clsuffix = clsuffix
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261 if self.args.parampass == "positional":
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262 self.clpositional()
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263 else:
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264 self.clargparse()
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265
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266 def prepScript(self):
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267 rx = open(self.args.script_path, "r").readlines()
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268 rx = [x.rstrip() for x in rx]
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269 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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270 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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271 self.script = "\n".join(rx)
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272 fhandle, self.sfile = tempfile.mkstemp(
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273 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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274 )
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275 tscript = open(self.sfile, "w")
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276 tscript.write(self.script)
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277 tscript.close()
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278 self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx])
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279 self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
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280 art = "%s.%s" % (self.tool_name, self.executeme)
48
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281 artifact = open(art, "wb")
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282 artifact.write(bytes(self.script, "utf8"))
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parents:
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283 artifact.close()
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parents:
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284
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285 def cleanuppar(self):
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parents:
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286 """ positional parameters are complicated by their numeric ordinal"""
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parents:
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287 for i, p in enumerate(self.infiles):
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parents:
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288 if self.args.parampass == "positional":
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parents:
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289 assert p[ICLPOS].isdigit(), (
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parents:
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290 "Positional parameters must be ordinal integers - got %s for %s"
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parents:
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291 % (p[ICLPOS], p[ILABPOS])
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parents:
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292 )
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parents:
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293 p.append(p[ICLPOS])
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parents:
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294 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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parents:
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295 scl = "input%d" % (i + 1)
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parents:
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296 p[ICLPOS] = scl
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parents:
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297 self.infiles[i] = p
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parents:
diff changeset
298 for i, p in enumerate(
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parents:
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299 self.outfiles
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parents:
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300 ): # trying to automagically gather using extensions
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fubar
parents:
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301 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
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parents:
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302 assert p[OCLPOS].isdigit(), (
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fubar
parents:
diff changeset
303 "Positional parameters must be ordinal integers - got %s for %s"
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fubar
parents:
diff changeset
304 % (p[OCLPOS], p[ONAMEPOS])
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parents:
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305 )
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parents:
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306 p.append(p[OCLPOS])
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fubar
parents:
diff changeset
307 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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parents:
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308 scl = p[ONAMEPOS]
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fubar
parents:
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309 p[OCLPOS] = scl
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parents:
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310 self.outfiles[i] = p
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parents:
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311 for i, p in enumerate(self.addpar):
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parents:
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312 if self.args.parampass == "positional":
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parents:
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313 assert p[ACLPOS].isdigit(), (
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parents:
diff changeset
314 "Positional parameters must be ordinal integers - got %s for %s"
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parents:
diff changeset
315 % (p[ACLPOS], p[ANAMEPOS])
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parents:
diff changeset
316 )
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parents:
diff changeset
317 p.append(p[ACLPOS])
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fubar
parents:
diff changeset
318 if p[ACLPOS].isdigit():
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fubar
parents:
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319 scl = "input%s" % p[ACLPOS]
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fubar
parents:
diff changeset
320 p[ACLPOS] = scl
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fubar
parents:
diff changeset
321 self.addpar[i] = p
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fubar
parents:
diff changeset
322
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parents:
diff changeset
323 def clsimple(self):
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parents:
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324 """ no parameters - uses < and > for i/o
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parents:
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325 """
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parents:
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326 aCL = self.cl.append
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parents:
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327 aXCL = self.xmlcl.append
62
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fubar
parents: 57
diff changeset
328
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fubar
parents: 57
diff changeset
329 if len(self.infiles) > 0:
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parents: 57
diff changeset
330 aCL("<")
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parents: 57
diff changeset
331 aCL(self.infiles[0][IPATHPOS])
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fubar
parents: 57
diff changeset
332 aXCL("<")
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parents: 57
diff changeset
333 aXCL("$%s" % self.infiles[0][ICLPOS])
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fubar
parents: 57
diff changeset
334 if len(self.outfiles) > 0:
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fubar
parents: 57
diff changeset
335 aCL(">")
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fubar
parents: 57
diff changeset
336 aCL(self.outfiles[0][OCLPOS])
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fubar
parents: 57
diff changeset
337 aXCL(">")
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fubar
parents: 57
diff changeset
338 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
48
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fubar
parents:
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339
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parents:
diff changeset
340 def clpositional(self):
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parents:
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341 # inputs in order then params
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parents:
diff changeset
342 aCL = self.cl.append
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fubar
parents:
diff changeset
343 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
344 if " " in v:
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fubar
parents:
diff changeset
345 aCL("%s" % v)
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fubar
parents:
diff changeset
346 else:
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fubar
parents:
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347 aCL(v)
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parents:
diff changeset
348 aXCL = self.xmlcl.append
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fubar
parents:
diff changeset
349 for (o_v, k, v, koverride) in self.xclsuffix:
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fubar
parents:
diff changeset
350 aXCL(v)
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fubar
parents:
diff changeset
351 if self.lastxclredirect:
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fubar
parents:
diff changeset
352 aXCL(self.lastxclredirect[0])
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fubar
parents:
diff changeset
353 aXCL(self.lastxclredirect[1])
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fubar
parents:
diff changeset
354
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fubar
parents:
diff changeset
355 def clargparse(self):
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parents:
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356 """ argparse style
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fubar
parents:
diff changeset
357 """
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fubar
parents:
diff changeset
358 aCL = self.cl.append
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fubar
parents:
diff changeset
359 aXCL = self.xmlcl.append
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parents:
diff changeset
360 # inputs then params in argparse named form
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fubar
parents:
diff changeset
361 for (o_v, k, v, koverride) in self.xclsuffix:
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fubar
parents:
diff changeset
362 if koverride > "":
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fubar
parents:
diff changeset
363 k = koverride
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fubar
parents:
diff changeset
364 elif len(k.strip()) == 1:
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fubar
parents:
diff changeset
365 k = "-%s" % k
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fubar
parents:
diff changeset
366 else:
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fubar
parents:
diff changeset
367 k = "--%s" % k
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fubar
parents:
diff changeset
368 aXCL(k)
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fubar
parents:
diff changeset
369 aXCL(v)
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fubar
parents:
diff changeset
370 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
371 if koverride > "":
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fubar
parents:
diff changeset
372 k = koverride
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fubar
parents:
diff changeset
373 elif len(k.strip()) == 1:
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fubar
parents:
diff changeset
374 k = "-%s" % k
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fubar
parents:
diff changeset
375 else:
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fubar
parents:
diff changeset
376 k = "--%s" % k
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fubar
parents:
diff changeset
377 aCL(k)
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fubar
parents:
diff changeset
378 aCL(v)
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fubar
parents:
diff changeset
379
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fubar
parents:
diff changeset
380 def getNdash(self, newname):
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fubar
parents:
diff changeset
381 if self.is_positional:
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fubar
parents:
diff changeset
382 ndash = 0
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fubar
parents:
diff changeset
383 else:
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fubar
parents:
diff changeset
384 ndash = 2
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fubar
parents:
diff changeset
385 if len(newname) < 2:
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fubar
parents:
diff changeset
386 ndash = 1
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fubar
parents:
diff changeset
387 return ndash
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fubar
parents:
diff changeset
388
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fubar
parents:
diff changeset
389 def doXMLparam(self):
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fubar
parents:
diff changeset
390 """flake8 made me do this..."""
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fubar
parents:
diff changeset
391 for p in self.outfiles:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
392 newname, newfmt, newcl, test, oldcl = p
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
393 ndash = self.getNdash(newcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
394 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397 if oldcl == "STDOUT":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 aparm.positional = 9999999
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 aparm.command_line_override = "> $%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 aparm.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 aparm.command_line_override = "$%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
404 usetest = None
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
405 ld = None
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
406 if test > "":
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
407 if test.startswith("diff"):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
408 usetest = "diff"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
409 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
410 ld = int(test.split(":")[1])
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
411 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
412 usetest = test
50
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fubar
parents: 49
diff changeset
413 tp = gxtp.TestOutput(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
414 name=newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
415 value="%s_sample" % newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
416 format=newfmt,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
417 compare=usetest,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
418 lines_diff=ld,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
419 delta=None,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
420 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
421 self.testparam.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
422 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
423 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
424 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
425 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
426 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
427 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
428 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
429 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
430 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
431 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
432 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
434 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
435 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
436 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
438 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 for p in self.addpar:
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fubar
parents:
diff changeset
444 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 aninput.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 self.tinputs.append(aparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 self.tparm = gxtp.TestParam(newname, value=newval)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
486 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
487 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
488 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
489 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
490 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
491 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
492 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
493 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
494 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
495 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
496 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
497 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
498 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
499 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
500 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
501 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
502 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
503 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
504 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
505 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
506 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
507 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
508 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
509 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
510 self.testparam.append(tp)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
511 if len(self.outfiles > 0):
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
512 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
513 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
514 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
515 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
516 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
517 self.toutputs.append(anout)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
518 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
519 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
520
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
521 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
522 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
523 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
524 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
525 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
526 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
527 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
528 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
529 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
530 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
531 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
532 helptext = open(self.args.help_text, "r").readlines()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
533 safertext = [html_escape(x) for x in helptext]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
534 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
535 scrpt = self.script.split('\n')
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
536 scrpt.insert(0,"```\n")
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
537 if len(scrpt) > 300:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
538 safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
539 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
540 safertext = safertext + scrpt
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
541 safertext.append("\n```")
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
542 self.newtool.help = "\n".join([x for x in safertext])
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
543 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
544 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
545 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
546 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
547 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
548 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
549 self.newtool.version_command = None # do not want
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
550 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
551 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
552 for d in self.args.packages.split(","):
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
553 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
554 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
555 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
556 packg = d
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
557 ver = ""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
558 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
559 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
560 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
561 self.newtool.requirements = requirements
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
562 if self.args.parampass == "0":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
563 self.doNoXMLparam()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
564 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
565 self.doXMLparam()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
566 self.newtool.outputs = self.toutputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
567 self.newtool.inputs = self.tinputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
568 if self.args.script_path:
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
569 configfiles = gxtp.Configfiles()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
570 configfiles.append(gxtp.Configfile(name="runme", text=self.script))
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
571 self.newtool.configfiles = configfiles
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
572 tests = gxtp.Tests()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
573 test_a = gxtp.Test()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
574 for tp in self.testparam:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
575 test_a.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
576 tests.append(test_a)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
577 self.newtool.tests = tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
578 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
579 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
580 % (self.args.user_email, timenow())
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
581 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
582 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
583 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
584 "Cite: Creating re-usable tools from scripts doi: \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
585 10.1093/bioinformatics/bts573"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
586 )
50
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fubar
parents: 49
diff changeset
587 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
588 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
589 if (
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
590 self.test_override
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fubar
parents: 49
diff changeset
591 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
592 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
593 part2 = exml.split("</tests>")[1]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
594 fixed = "%s\n%s\n%s" % (part1, self.test_override, part2)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
595 exml = fixed
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
596 xf = open("%s.xml" % self.tool_name, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
597 xf.write(exml)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
598 xf.write("\n")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
599 xf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
600 # ready for the tarball
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
601
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fubar
parents:
diff changeset
602 def run(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
603 """
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
604 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
605 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
606 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
607 automagically selected
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
608 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
609 s = "run cl=%s" % str(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
610 logging.debug(s)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
611 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
612 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
613 if self.args.parampass != "0":
56
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fubar
parents: 51
diff changeset
614 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
615 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
616 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
617 ste = open(self.elog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
618 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
619 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
620 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
621 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
622 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
623 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
624 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
625 sto.write(
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
626 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
627 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
628 sto.flush()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
629 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
630 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
631 ste.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
632 retval = p.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
633 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
634 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
635 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
636 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
637 sti = sys.stdin
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
638 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
639 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
640 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
641 sto = sys.stdout
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
642 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
643 retval = p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
644 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
645 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
646 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
647 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
648 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
649 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
650 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
651 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
652 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
653 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
654
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
655 def planemo_shedload(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
656 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
657 planemo shed_create --shed_target testtoolshed
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
658 planemo shed_update --check_diff --shed_target testtoolshed
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
659 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
660 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
661 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
662 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
663 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
664 cll = ["planemo", "shed_create", "--shed_target", "local"]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
665 try:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
666 p = subprocess.run(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
667 cll, shell=True, cwd=self.tooloutdir, stdout=tout, stderr=tout
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
668 )
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
669 except:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
670 pass
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
671 if p.returncode != 0:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
672 print("Repository %s exists" % self.args.tool_name)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
673 else:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
674 print("initiated %s" % self.args.tool_name)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
675 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
676 "planemo",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
677 "shed_upload",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
678 "--shed_target",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
679 "local",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
680 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
681 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
682 "--name",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
683 self.args.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
684 "--shed_key",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
685 self.args.toolshed_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
686 "--tar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
687 self.newtarpath,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
688 ]
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
689 p = subprocess.run(cll, shell=False)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
690 print("Ran", " ".join(cll), "got", p.returncode)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
691 tout.close()
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
692 return p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
693
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
694 def planemo_test(self, genoutputs=True):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
695 """planemo is a requirement so is available for testing
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
696 and for generating test outputs if command or test overrides are supplied
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
697 test outputs are sent to repdir for display
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
698 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
699 xreal = "%s.xml" % self.tool_name
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
700 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
701 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
702 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
703 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
704 if genoutputs:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
705 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
706 "planemo",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
707 "test",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
708 "--galaxy_root",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
709 self.args.galaxy_root,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
710 "--update_test_data",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
711 xreal,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
712 ]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
713 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
714 cll = ["planemo", "test", "--galaxy_root",
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
715 self.args.galaxy_root,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
716 xreal,]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
717 p = subprocess.run(
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
718 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
719 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
720 if genoutputs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
721 with os.scandir(self.testdir) as outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
722 for entry in outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
723 if entry.is_file():
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
724 dest = os.path.join(self.repdir, entry.name)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
725 src = os.path.join(self.testdir, entry.name)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
726 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
727 tout.write(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
728 "Copied output %s to %s after planemo test\n" % (src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
729 )
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
730 tout.close()
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
731 return p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
732
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
733 def eph_galaxy_load(self):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
734 """load the new tool from the local toolshed after planemo uploads it
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
735 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
736 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
737 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
738 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
739 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
740 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
741 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
742 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
743 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
744 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
745 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
746 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
747 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
748 "--name",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
749 self.args.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
750 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
751 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
752 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
753 self.args.toolshed_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
754 "--section_label",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
755 "Generated Tools",
51
4b71b252eacb Uploaded
fubar
parents: 50
diff changeset
756
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
757 ]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
758 print("running\n", " ".join(cll))
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
759 p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
760 if p.returncode != 0:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
761 print(
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
762 "Repository %s installation returned %d"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
763 % (self.args.tool_name, p.returncode)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
764 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
765 else:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
766 print("installed %s" % self.args.tool_name)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
767 tout.close()
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
768 return p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
769
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
770 def writeShedyml(self):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
771 """for planemo
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
772 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
773 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
774 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
775 yamlf = open(yfname, "w")
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diff changeset
776 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
777 "name": self.tool_name,
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diff changeset
778 "owner": yuser,
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diff changeset
779 "type": "unrestricted",
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diff changeset
780 "description": self.args.tool_desc,
50
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diff changeset
781 "synopsis": self.args.tool_desc,
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diff changeset
782 "category": "TF Generated Tools",
49
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783 }
48
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784 yaml.dump(odict, yamlf, allow_unicode=True)
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785 yamlf.close()
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786
50
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diff changeset
787 def makeTool(self):
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788 """write xmls and input samples into place
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789 """
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790 self.makeXML()
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791 if self.args.script_path:
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792 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
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793 if not os.path.exists(stname):
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794 shutil.copyfile(self.sfile, stname)
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795 xreal = "%s.xml" % self.tool_name
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diff changeset
796 xout = os.path.join(self.tooloutdir, xreal)
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797 shutil.copyfile(xreal, xout)
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diff changeset
798 for p in self.infiles:
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diff changeset
799 pth = p[IPATHPOS]
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800 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
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801 shutil.copyfile(pth, dest)
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802 dest = os.path.join(self.repdir, "%s.%s" % (p[ICLPOS], p[IFMTPOS]))
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diff changeset
803 shutil.copyfile(pth, dest)
49
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804
50
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diff changeset
805 def makeToolTar(self):
56
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806 """ move outputs into test-data and prepare the tarball
50
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807 """
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808 for p in self.outfiles:
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809 src = p[ONAMEPOS]
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810 if os.path.isfile(src):
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811 dest = os.path.join(self.testdir, "%s_sample" % src)
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diff changeset
812 shutil.copyfile(src, dest)
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diff changeset
813 dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS]))
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diff changeset
814 shutil.copyfile(src, dest)
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815 else:
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diff changeset
816 print(
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817 "### problem - output file %s not found in tooloutdir %s"
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818 % (src, self.tooloutdir)
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819 )
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820 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
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821 tf = tarfile.open(self.newtarpath, "w:gz")
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822 tf.add(name=self.tooloutdir, arcname=self.tool_name)
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823 tf.close()
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824 shutil.copyfile(self.newtarpath, self.args.new_tool)
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825
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826 def moveRunOutputs(self):
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827 """need to move planemo or run outputs into toolfactory collection
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828 """
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829 with os.scandir(self.tooloutdir) as outs:
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830 for entry in outs:
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831 if not entry.is_file() or entry.name.startswith("."):
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832 continue
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833 if "." in entry.name:
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834 nayme, ext = os.path.splitext(entry.name)
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835 else:
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836 ext = ".txt"
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837 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
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838 dest = os.path.join(self.repdir, ofn)
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839 src = os.path.join(self.tooloutdir, entry.name)
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diff changeset
840 shutil.copyfile(src, dest)
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diff changeset
841
49
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842
48
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843 def main():
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844 """
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845 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
49
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846 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
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diff changeset
847 --tool_name "foo" --interpreter "Rscript"
48
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848 </command>
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849 """
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850 parser = argparse.ArgumentParser()
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851 a = parser.add_argument
49
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852 a("--script_path", default=None)
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853 a("--history_test", default=None)
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854 a("--cl_prefix", default=None)
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855 a("--sysexe", default=None)
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856 a("--packages", default=None)
48
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857 a("--tool_name", default=None)
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diff changeset
858 a("--input_files", default=[], action="append")
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859 a("--output_files", default=[], action="append")
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860 a("--user_email", default="Unknown")
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diff changeset
861 a("--bad_user", default=None)
49
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diff changeset
862 a("--make_Tool", default="runonly")
48
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863 a("--help_text", default=None)
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864 a("--tool_desc", default=None)
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diff changeset
865 a("--tool_version", default=None)
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diff changeset
866 a("--citations", default=None)
49
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diff changeset
867 a("--command_override", default=None)
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868 a("--test_override", default=None)
48
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869 a("--additional_parameters", action="append", default=[])
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870 a("--edit_additional_parameters", action="store_true", default=False)
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diff changeset
871 a("--parampass", default="positional")
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diff changeset
872 a("--tfout", default="./tfout")
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diff changeset
873 a("--new_tool", default="new_tool")
49
35a912ce0c83 Can now make the bwa example from planemo :)
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874 a("--galaxy_url", default="http://localhost:8080")
50
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diff changeset
875 a("--galaxy_api_key", default="fakekey")
48
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diff changeset
876 a("--toolshed_url", default="http://localhost:9009")
50
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diff changeset
877 a("--toolshed_api_key", default="fakekey")
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diff changeset
878 a("--galaxy_root", default="/galaxy-central")
48
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879
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diff changeset
880 args = parser.parse_args()
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881 assert not args.bad_user, (
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diff changeset
882 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file'
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883 % (args.bad_user, args.bad_user)
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diff changeset
884 )
49
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885 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
48
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886 assert (
49
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887 args.sysexe or args.packages
48
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888 ), "## Tool Factory wrapper expects an interpreter or an executable package"
49
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diff changeset
889 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
48
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diff changeset
890 # remove quotes we need to deal with spaces in CL params
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891 for i, x in enumerate(args.additional_parameters):
49
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diff changeset
892 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
48
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diff changeset
893 r = ScriptRunner(args)
49
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diff changeset
894 r.writeShedyml()
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895 r.makeTool()
50
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diff changeset
896 if args.command_override or args.test_override:
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diff changeset
897 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR
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diff changeset
898 r.moveRunOutputs()
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diff changeset
899 r.makeToolTar()
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diff changeset
900 retcode = r.planemo_test(genoutputs=False)
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diff changeset
901 r.moveRunOutputs()
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902 if args.make_Tool == "gentestinstall":
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903 r.planemo_shedload()
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diff changeset
904 r.eph_galaxy_load()
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diff changeset
905 else:
49
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906 retcode = r.run()
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diff changeset
907 if retcode:
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diff changeset
908 sys.stderr.write(
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diff changeset
909 "## Run failed with return code %d. Cannot build yet. Please fix and retry"
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diff changeset
910 % retcode
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diff changeset
911 )
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diff changeset
912 sys.exit(1)
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diff changeset
913 else:
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diff changeset
914 r.moveRunOutputs()
50
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915 r.makeToolTar()
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diff changeset
916 if args.make_Tool in ["gentestinstall", "gentest"]:
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diff changeset
917 r.planemo_test(genoutputs=False)
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diff changeset
918 r.moveRunOutputs()
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919 if args.make_Tool == "gentestinstall":
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920 r.planemo_shedload()
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diff changeset
921 r.eph_galaxy_load()
48
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diff changeset
922
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diff changeset
923
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924 if __name__ == "__main__":
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925 main()