comparison toolfactory/rgToolFactory2.xml @ 46:f8700bed1e17 draft

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45:668c37cc8962

              help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root and so on. " value="" />

        </repeat>
     </xml>
     <xml name="builtin_dynpar">
          <param name="interpreter_version" type="text" value=""
          label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/>
            <param name="exe_package_version" type="text" value=""
              label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/>
          <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True"
              help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
          </param>
    </xml>
    <xml name="dynpar">
          <param name="interpreter_version" type="text" value=""
          label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/>
            <param name="exe_package_version" type="text" value=""
              label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/>
          <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True"
              help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>

#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
#if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
 #else:
$__tool_directory__/rgToolFactory2.py
--runmode "$interexe.interpreter"
   #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system":
--exe_package="$interexe.exe_package"
    #if str($interexe.exe_package_version) != 'None' :
--exe_package_version="$interexe.exe_package_version"
    #end if
   #else:
--interpreter_name="$interexe.interpreter" --script_path "$runme"
     #if str($interexe.interpreter_version) != 'None':

     #end if
     #for apar in $ppass.additional_parameters:
--additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
     #end for
   #end if

     #for $intab in $ppass.history_inputs:
--input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
     #end for


     #for $otab in $ppass.history_outputs:
--output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL"
     #end for
 #end if
]]></command>

            <option value="r-base">Rscript</option>
            <option value="perl">perl</option>
            <option value="bash">bash</option>
            <option value="sh">sh</option>
            <option value="system" >A system executable found on the path such as awk/sed</option>
            <option value="specialtestcaseinterpreterpython" >for testing only - do not use me please</option>
        </param>
        <when value="Executable">
            <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" optional="false"/>
            <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" />
        </when>
        <when value="system">
            <param name="exe_package" type="text" value="" label="System executable to run"  optional="false"/>
            <param name="exe_package_version" type="text" value=""
              label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty"/>
        </when>
        <when value = "python">
           <expand macro="dynpar" />
        </when>
        <when value = "r-base">

        </when>
        <when value = "bash">
           <expand macro="builtin_dynpar" />
        </when>
        <when value = "sh">
           <expand macro="builtin_dynpar" />
        </when>
         <when value = "specialtestcaseinterpreterpython">
           <expand macro="builtin_dynpar" />
        </when>
    </conditional>
    <conditional name = "ppass">

46:f8700bed1e17

              help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root and so on. " value="" />

        </repeat>
     </xml>
     <xml name="builtin_dynpar">
            <param name="exe_package" type="hidden" value="" />
            <param name="exe_package_version" type="hidden" value="" />
            <param name="cl_override" type="hidden" value="" />
            <param name="interpreter_version" type="hidden" value=""/>
            <param name="dependencies" type="hidden" value="" />
          <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True"
              help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
          </param>
    </xml>
    <xml name="dynpar">
            <param name="exe_package" type="hidden" value="" />
            <param name="exe_package_version" type="hidden" value="" />
            <param name="cl_override" type="hidden" value="" />
            <param name="dependencies" type="text" value="" label="List additional dependencies - e.g. 'planemo, ephemeris'" help="These will be managed by Conda" />
          <param name="interpreter_version" type="text" value=""
          label="Specific interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty"/>
          <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="Script goes here" area="True"
              help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>

#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
#if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
 #else:
$__tool_directory__/rgToolFactory2.py
--dependencies "$interexe.dependencies"
--runmode "$interexe.interpreter"
   #if len(str($interexe.cl_override)) > 0:
--cl_override "$interexe.cl_override"
   #end if
   #if str($interexe.interpreter)=="Executable" or str($interexe.interpreter)=="system":
--exe_package="$interexe.exe_package"
    #if $interexe.exe_package_version:
--exe_package_version="$interexe.exe_package_version"
    #end if
   #else:
--interpreter_name="$interexe.interpreter" --script_path "$runme"
     #if str($interexe.interpreter_version) != 'None':

     #end if
     #for apar in $ppass.additional_parameters:
--additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
     #end for
   #end if
     #for $intab in $ppass.history_inputs:
--input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
     #end for
     #for $otab in $ppass.history_outputs:
--output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL"
     #end for
 #end if
]]></command>

            <option value="r-base">Rscript</option>
            <option value="perl">perl</option>
            <option value="bash">bash</option>
            <option value="sh">sh</option>
            <option value="system" >A system executable found on the path such as awk/sed</option>
        </param>
        <when value="Executable">
            <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" optional="false"/>
            <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" />
            <param name="cl_override" type="text" value="" label="Command line override prefix - e.g. for ephemeris prepend the specific function such as 'workflow_install'" 
             help="Some packages like ephemerisand planemo require a sub-command - eg planemo test - before parameters are passed. Supply that here"/>
            <param name="dependencies" type="hidden" value="" />
        </when>
        <when value="system">
            <param name="dependencies" type="hidden" value="" />
            <param name="exe_package" type="text" value="" label="System executable to run - e.g. awk"/>
            <param name="exe_package_version" type="hidden" value="" />
            <param name="cl_override" type="hidden" value="" />
        </when>
        <when value = "python">
           <expand macro="dynpar" />
        </when>
        <when value = "r-base">

        </when>
        <when value = "bash">
           <expand macro="builtin_dynpar" />
        </when>
        <when value = "sh">
           <expand macro="builtin_dynpar" />
        </when>
    </conditional>
    <conditional name = "ppass">