Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.xml @ 119:8ea1133b9d9a draft
Uploaded
author | fubar |
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date | Tue, 05 Jan 2021 00:34:48 +0000 |
parents | e43c43396a70 |
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118:e43c43396a70 | 119:8ea1133b9d9a |
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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> |