Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.xml @ 108:e878bfc6b80c draft

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Uploaded
author fubar
date Sun, 29 Nov 2020 04:32:22 +0000
parents 557d5f06f213
children 223b78754735
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107:18e616939a91 108:e878bfc6b80c
77 </options> 77 </options>
78 </param> 78 </param>
79 <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required." 79 <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required."
80 help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/> 80 help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/>
81 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" 81 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation"
82 help="Available options are diff:lines, sim_size" value="diff:2"/> 82 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="sim_size:0.01"/>
83 </repeat> 83 </repeat>
84 </xml> 84 </xml>
85 <xml name="additparam"> 85 <xml name="additparam">
86 <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?" 86 <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?"
87 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> 87 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
230 </configfiles> 230 </configfiles>
231 <inputs> 231 <inputs>
232 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs" 232 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
233 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only"> 233 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
234 <sanitizer invalid_char=""> 234 <sanitizer invalid_char="">
235 <valid initial="string.letters,string.digits"> 235 <valid initial="string.ascii_lowercase,string.digits">
236 <add value="_"/> 236 <add value="_"/>
237 </valid> 237 </valid>
238 </sanitizer> 238 </sanitizer>
239 </param> 239 </param>
240 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes" 240 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
241 optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" /> 241 optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" />
242 242
243 <conditional name="usescript"> 243 <conditional name="usescript">
244 <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash" 244 <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash"
245 help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> 245 help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them">
246 <option value="no" selected="true">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> 246 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
247 <option value="yes">Yes, a script is ready to be pasted below</option> 247 <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
248 </param> 248 </param>
249 <when value="no"> 249 <when value="no">
250 <param name="dynScript" type="hidden" value="" /> 250 <param name="dynScript" type="hidden" value="" />
251 <param name="scriptrunner" type="hidden" value="" /> 251 <param name="scriptrunner" type="hidden" value="" />
252 </when> 252 </when>
322 322
323 <conditional name="makeMode"> 323 <conditional name="makeMode">
324 <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation" 324 <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation"
325 help="Installation in this Galaxy is optional" > 325 help="Installation in this Galaxy is optional" >
326 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> 326 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
327 <option value="gentest" selected="true">Test with planemo after generating.</option> 327 <option value="gentest">Test with planemo after generating.</option>
328 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> 328 <option value="gentestinstall" selected="true">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
329 </param> 329 </param>
330 <when value="generate"> 330 <when value="generate">
331 <param name="galaxy_apikey" value="" type="hidden" ></param> 331 <param name="galaxy_apikey" value="" type="hidden" ></param>
332 <param name="toolshed_apikey" value="" type="hidden" ></param> 332 <param name="toolshed_apikey" value="" type="hidden" ></param>
333 <param name="galaxy_url" value="" type="hidden" ></param> 333 <param name="galaxy_url" value="" type="hidden" ></param>