Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.xml @ 46:f8700bed1e17 draft

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author fubar
date Tue, 18 Aug 2020 08:25:43 -0400
parents e7e9732ebed6
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45:668c37cc8962 46:f8700bed1e17
90 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root and so on. " value="" /> 90 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root and so on. " value="" />
91 91
92 </repeat> 92 </repeat>
93 </xml> 93 </xml>
94 <xml name="builtin_dynpar"> 94 <xml name="builtin_dynpar">
95 <param name="interpreter_version" type="text" value="" 95 <param name="exe_package" type="hidden" value="" />
96 label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/> 96 <param name="exe_package_version" type="hidden" value="" />
97 <param name="exe_package_version" type="text" value="" 97 <param name="cl_override" type="hidden" value="" />
98 label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> 98 <param name="interpreter_version" type="hidden" value=""/>
99 <param name="dependencies" type="hidden" value="" />
99 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True" 100 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True"
100 help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> 101 help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
101 <sanitizer> 102 <sanitizer>
102 <valid initial="string.printable"> 103 <valid initial="string.printable">
103 </valid> 104 </valid>
104 <mapping initial="none"/> 105 <mapping initial="none"/>
105 </sanitizer> 106 </sanitizer>
106 </param> 107 </param>
107 </xml> 108 </xml>
108 <xml name="dynpar"> 109 <xml name="dynpar">
110 <param name="exe_package" type="hidden" value="" />
111 <param name="exe_package_version" type="hidden" value="" />
112 <param name="cl_override" type="hidden" value="" />
113 <param name="dependencies" type="text" value="" label="List additional dependencies - e.g. 'planemo, ephemeris'" help="These will be managed by Conda" />
109 <param name="interpreter_version" type="text" value="" 114 <param name="interpreter_version" type="text" value=""
110 label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/> 115 label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/>
111 <param name="exe_package_version" type="text" value=""
112 label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/>
113 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True" 116 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True"
114 help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> 117 help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
115 <sanitizer> 118 <sanitizer>
116 <valid initial="string.printable"> 119 <valid initial="string.printable">
117 </valid> 120 </valid>
129 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' 132 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
130 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ): 133 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
131 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ 134 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
132 #else: 135 #else:
133 $__tool_directory__/rgToolFactory2.py 136 $__tool_directory__/rgToolFactory2.py
137 --dependencies "$interexe.dependencies"
134 --runmode "$interexe.interpreter" 138 --runmode "$interexe.interpreter"
139 #if len(str($interexe.cl_override)) > 0:
140 --cl_override "$interexe.cl_override"
141 #end if
135 #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system": 142 #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system":
136 --exe_package="$interexe.exe_package" 143 --exe_package="$interexe.exe_package"
137 #if str($interexe.exe_package_version) != 'None' : 144 #if $interexe.exe_package_version:
138 --exe_package_version="$interexe.exe_package_version" 145 --exe_package_version="$interexe.exe_package_version"
139 #end if 146 #end if
140 #else: 147 #else:
141 --interpreter_name="$interexe.interpreter" --script_path "$runme" 148 --interpreter_name="$interexe.interpreter" --script_path "$runme"
142 #if str($interexe.interpreter_version) != 'None': 149 #if str($interexe.interpreter_version) != 'None':
157 #end if 164 #end if
158 #for apar in $ppass.additional_parameters: 165 #for apar in $ppass.additional_parameters:
159 --additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" 166 --additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
160 #end for 167 #end for
161 #end if 168 #end if
162
163 #for $intab in $ppass.history_inputs: 169 #for $intab in $ppass.history_inputs:
164 --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" 170 --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
165 #end for 171 #end for
166
167
168 #for $otab in $ppass.history_outputs: 172 #for $otab in $ppass.history_outputs:
169 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL" 173 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL"
170 #end for 174 #end for
171 #end if 175 #end if
172 ]]></command> 176 ]]></command>
218 <option value="r-base">Rscript</option> 222 <option value="r-base">Rscript</option>
219 <option value="perl">perl</option> 223 <option value="perl">perl</option>
220 <option value="bash">bash</option> 224 <option value="bash">bash</option>
221 <option value="sh">sh</option> 225 <option value="sh">sh</option>
222 <option value="system" >A system executable found on the path such as awk/sed</option> 226 <option value="system" >A system executable found on the path such as awk/sed</option>
223 <option value="specialtestcaseinterpreterpython" >for testing only - do not use me please</option>
224 </param> 227 </param>
225 <when value="Executable"> 228 <when value="Executable">
226 <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" optional="false"/> 229 <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" optional="false"/>
227 <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" /> 230 <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" />
231 <param name="cl_override" type="text" value="" label="Command line override prefix - e.g. for ephemeris prepend the specific function such as 'workflow_install'"
232 help="Some packages like ephemerisand planemo require a sub-command - eg planemo test - before parameters are passed. Supply that here"/>
233 <param name="dependencies" type="hidden" value="" />
228 </when> 234 </when>
229 <when value="system"> 235 <when value="system">
230 <param name="exe_package" type="text" value="" label="System executable to run" optional="false"/> 236 <param name="dependencies" type="hidden" value="" />
231 <param name="exe_package_version" type="text" value="" 237 <param name="exe_package" type="text" value="" label="System executable to run - e.g. awk"/>
232 label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/> 238 <param name="exe_package_version" type="hidden" value="" />
239 <param name="cl_override" type="hidden" value="" />
233 </when> 240 </when>
234 <when value = "python"> 241 <when value = "python">
235 <expand macro="dynpar" /> 242 <expand macro="dynpar" />
236 </when> 243 </when>
237 <when value = "r-base"> 244 <when value = "r-base">
242 </when> 249 </when>
243 <when value = "bash"> 250 <when value = "bash">
244 <expand macro="builtin_dynpar" /> 251 <expand macro="builtin_dynpar" />
245 </when> 252 </when>
246 <when value = "sh"> 253 <when value = "sh">
247 <expand macro="builtin_dynpar" />
248 </when>
249 <when value = "specialtestcaseinterpreterpython">
250 <expand macro="builtin_dynpar" /> 254 <expand macro="builtin_dynpar" />
251 </when> 255 </when>
252 </conditional> 256 </conditional>
253 <conditional name = "ppass"> 257 <conditional name = "ppass">
254 258