Mercurial > repos > fubar > tool_factory_2
diff toolfactory/rgToolFactory2.xml @ 119:8ea1133b9d9a draft
Uploaded
author | fubar |
---|---|
date | Tue, 05 Jan 2021 00:34:48 +0000 |
parents | e43c43396a70 |
children |
line wrap: on
line diff
--- a/toolfactory/rgToolFactory2.xml Fri Dec 11 04:23:48 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Tue Jan 05 00:34:48 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="rgtfd" name="toolfactory" version="2.00" profile="16.04" > +<tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" > <description>Scripts into tools v2.0</description> <macros> <xml name="tool_metadata"> @@ -73,8 +73,9 @@ <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help="No spaces! Argparse will also use this name as --[name]"> <sanitizer invalid_char="_"> - <valid initial="string.letters,string.digits"/> - <add value="_" /> + <valid initial="string.ascii_letters,string.digits"> + <add value="_" /> + </valid> </sanitizer> </param> <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" @@ -134,7 +135,7 @@ </param> <param name="param_CL" type="text" label="Positional ordinal | argparse argument name" 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="" /> - <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" + <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ~~--foo if needed" help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> </repeat> </section> @@ -145,8 +146,7 @@ <requirement type="package" version="0.4.11">galaxyxml</requirement> <requirement type="package" version="0.14.0">bioblend</requirement> <requirement type="package" version="0.10.6">ephemeris</requirement> - <requirement type="package" version="4.4.0">docker-py</requirement> - <requirement type="package" version="0.72.0">planemo</requirement> + <requirement type="package" version="0.74.1">planemo</requirement> </requirements> <command ><![CDATA[ @@ -173,7 +173,6 @@ --sysexe "$deps.usescript.scriptrunner" #end if --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass" - #if str($make.makeMode.make_Tool)!="runonly": --make_Tool "$make.makeMode.make_Tool" --tool_desc "$make.makeMode.tool_desc" @@ -267,7 +266,7 @@ <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" 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"> <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> + <valid initial="string.ascii_letters,string.digits"> <add value="_"/> </valid> </sanitizer> @@ -339,8 +338,8 @@ <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" help="Installation in this Galaxy is optional" > <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> - <option value="gentest">Test with planemo after generating.</option> - <option value="gentestinstall" selected="true">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> + <option value="gentest" selected="true">Test with planemo after generating.</option> + <option value="gentestinstall">Install in Galaxy after generation and testing. URLs and matching API keys are required for this step! </option> </param> <when value="generate"> <param name="galaxy_apikey" value="" type="hidden" ></param>