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

Uploaded

--- 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>