Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.xml @ 119:8ea1133b9d9a draft

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author fubar
date Tue, 05 Jan 2021 00:34:48 +0000
parents e43c43396a70
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118:e43c43396a70 119:8ea1133b9d9a
1 <tool id="rgtfd" name="toolfactory" version="2.00" profile="16.04" > 1 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
2 <description>Scripts into tools v2.0</description> 2 <description>Scripts into tools v2.0</description>
3 <macros> 3 <macros>
4 <xml name="tool_metadata"> 4 <xml name="tool_metadata">
5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" 5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
6 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> 6 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
71 <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs" 71 <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs"
72 help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> 72 help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
73 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" 73 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false"
74 help="No spaces! Argparse will also use this name as --[name]"> 74 help="No spaces! Argparse will also use this name as --[name]">
75 <sanitizer invalid_char="_"> 75 <sanitizer invalid_char="_">
76 <valid initial="string.letters,string.digits"/> 76 <valid initial="string.ascii_letters,string.digits">
77 <add value="_" /> 77 <add value="_" />
78 </valid>
78 </sanitizer> 79 </sanitizer>
79 </param> 80 </param>
80 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" 81 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
81 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> 82 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
82 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 83 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
132 <mapping initial="none"/> 133 <mapping initial="none"/>
133 </sanitizer> 134 </sanitizer>
134 </param> 135 </param>
135 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name" 136 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
136 help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" /> 137 help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value="" />
137 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" 138 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ~~--foo if needed"
138 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> 139 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
139 </repeat> 140 </repeat>
140 </section> 141 </section>
141 </xml> 142 </xml>
142 </macros> 143 </macros>
143 144
144 <requirements> 145 <requirements>
145 <requirement type="package" version="0.4.11">galaxyxml</requirement> 146 <requirement type="package" version="0.4.11">galaxyxml</requirement>
146 <requirement type="package" version="0.14.0">bioblend</requirement> 147 <requirement type="package" version="0.14.0">bioblend</requirement>
147 <requirement type="package" version="0.10.6">ephemeris</requirement> 148 <requirement type="package" version="0.10.6">ephemeris</requirement>
148 <requirement type="package" version="4.4.0">docker-py</requirement> 149 <requirement type="package" version="0.74.1">planemo</requirement>
149 <requirement type="package" version="0.72.0">planemo</requirement>
150 </requirements> 150 </requirements>
151 151
152 <command ><![CDATA[ 152 <command ><![CDATA[
153 #import os 153 #import os
154 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' 154 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
171 #if $deps.usescript.choosescript == "yes": 171 #if $deps.usescript.choosescript == "yes":
172 --script_path "$runme" 172 --script_path "$runme"
173 --sysexe "$deps.usescript.scriptrunner" 173 --sysexe "$deps.usescript.scriptrunner"
174 #end if 174 #end if
175 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass" 175 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass"
176
177 #if str($make.makeMode.make_Tool)!="runonly": 176 #if str($make.makeMode.make_Tool)!="runonly":
178 --make_Tool "$make.makeMode.make_Tool" 177 --make_Tool "$make.makeMode.make_Tool"
179 --tool_desc "$make.makeMode.tool_desc" 178 --tool_desc "$make.makeMode.tool_desc"
180 --tool_version "$make.makeMode.tool_version" 179 --tool_version "$make.makeMode.tool_version"
181 --help_text "$helpme" 180 --help_text "$helpme"
265 </when> 264 </when>
266 <when value="yes"> 265 <when value="yes">
267 <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable" 266 <param name="scriptrunner" type="text" value="" label="Interpreter for the script - eg bash or python. Can be one of the dependencies named above or a system executable"
268 help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts"> 267 help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts">
269 <sanitizer invalid_char=""> 268 <sanitizer invalid_char="">
270 <valid initial="string.letters,string.digits"> 269 <valid initial="string.ascii_letters,string.digits">
271 <add value="_"/> 270 <add value="_"/>
272 </valid> 271 </valid>
273 </sanitizer> 272 </sanitizer>
274 </param> 273 </param>
275 <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names " 274 <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names "
337 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true"> 336 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
338 <conditional name="makeMode"> 337 <conditional name="makeMode">
339 <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" 338 <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"
340 help="Installation in this Galaxy is optional" > 339 help="Installation in this Galaxy is optional" >
341 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> 340 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
342 <option value="gentest">Test with planemo after generating.</option> 341 <option value="gentest" selected="true">Test with planemo after generating.</option>
343 <option value="gentestinstall" selected="true">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> 342 <option value="gentestinstall">Install in Galaxy after generation and testing. URLs and matching API keys are required for this step! </option>
344 </param> 343 </param>
345 <when value="generate"> 344 <when value="generate">
346 <param name="galaxy_apikey" value="" type="hidden" ></param> 345 <param name="galaxy_apikey" value="" type="hidden" ></param>
347 <param name="toolshed_apikey" value="" type="hidden" ></param> 346 <param name="toolshed_apikey" value="" type="hidden" ></param>
348 <param name="galaxy_url" value="" type="hidden" ></param> 347 <param name="galaxy_url" value="" type="hidden" ></param>