comparison toolfactory/rgToolFactory2.xml @ 49:35a912ce0c83 draft

Can now make the bwa example from planemo :)

48:5a7a5b06bce0

<tool id="rgTF2" name="toolfactory" version="2.00" profile="16.04" >
  <description>Scripts into tools</description>
  <macros>
     <xml name="io">
        <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed"
             help="USE SMALL SAMPLES because these will be used for the new tool's test. The names will become a history item selector as input for users of the new tool you are making">
            <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false"
               help=""/>
            <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
              help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
               <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
                <column name="value" index="0"/>
               </options>
            </param>
            <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative"
             help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
            </param>
            <param name="input_help" type="text" value="parameter_help" label="This will become help text on the form."
             help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation">
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
            </param>
            <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
              help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value="">
            </param>
        </repeat>
        <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed"
             help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
            <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help=""/>
            <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
              help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
               <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
                <column name="value" index="0"/>
               </options>
            </param>
            <param name="history_CL" type="text"  label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required."
              help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/>
        </repeat>
     </xml>
     <xml name="additparam">
        <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?"
             help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
            <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
            <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
        </param>

        <repeat name="additional_parameters" title="Pass additional parameters to the script"
             help="See examples below to see how these can be parsed by scripts in the various languages">
          <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter">
            <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"/>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_type" type="select" label="Select the type for this parameter">
            <option value="text" selected="true">text</option>
            <option value="integer">integer</option>
            <option value="float">float</option>
          </param>
          <param name="param_value" type="text" value="" label="Enter this parameter's default value"
            help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form"
             help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_help" type="text" value="parameter_help" label="Help for this parameter"
             help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_CL" type="text" label="Positional ordinal or 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"
              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>
                 <mapping initial="none"/>
              </sanitizer>
          </param>
    </xml>
  </macros>
   <requirements>
      <requirement type="package">python</requirement>
      <requirement type="package">galaxyxml</requirement>
      <requirement type="package">planemo</requirement>
      <requirement type="package">yaml</requirement>
      <requirement type="package">lxml</requirement>
  </requirements>
  <command interpreter="python"><![CDATA[
#import os
#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($interexe.interpreter_version) != 'None':
--interpreter_version="$interexe.interpreter_version"
     #end if
   #end if
--tool_name="$tool_name"  --user_email="$__user_email__" --citations="$citeme"  --parampass="$ppass.parampass"
   #if str($makeMode.make_Tool)=="yes":
--planemo_test "$makeMode.planemo_test"
--make_Tool="$makeMode.make_Tool"
--tool_desc="$makeMode.tool_desc"
--tool_version="$makeMode.tool_version"
--help_text="$helpme"
--new_tool="$new_tool"
   #end if
   #if $ppass.parampass != '0':
     #if str($ppass.edit_params) == "yes":
--edit_additional_parameters
     #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>
 <configfiles>
  <configfile name="runme">

#if $interexe.interpreter != "Executable" and $interexe.interpreter != "system" :
${interexe.dynScript}
#else:
$tool_name
#end if
 </configfile>
 <configfile name="helpme">
    #if $makeMode.make_Tool == "yes":
${makeMode.help_text}
    #else
$tool_name help goes here
    #end if
 </configfile>
 <configfile name="citeme">
#if $makeMode.make_Tool == "yes":
    #for $citation in $makeMode.citations:
        #if $citation.citation_type.type == "bibtex":
            **ENTRY**bibtex
            ${citation.citation_type.bibtex}
        #else
            **ENTRY**doi
            ${citation.citation_type.doi}
        #end if
    #end for
#end if
 </configfile>
  </configfiles>
  <inputs>

   <param name="tool_name" type="text" value="tool1"   label="New tool ID and title for outputs"
         help="This will become the toolshed repository name so choose thoughtfully to avoid namespace clashes with other tool writers. lower case, digits and underscores only">
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits">
                <add value="_"/>
            </valid>
        </sanitizer>
    </param>
    <conditional name="interexe">
        <param name="interpreter" type="select" label="Tool model: For a managed external dependency, choose 'Executable', or choose an interpreter for a script"
        help = "If executable, the supplied package will become a requirement so must match the tool dependency resolver package name - conda is the default.">
            <option value="Executable" selected="true">An executable binary to be provided and managed by the Conda dependency management subsystem</option>
            <option value="python">Use Python to run the script pasted below</option>
            <option value="r-base">Use R (Rscript) to run the script pasted below</option>
            <option value="perl">Use a depency managed Perl to run the script pasted below</option>
            <option value="bash">Use the system bash to run the script pasted below</option>
            <option value="sh">Use sh to run the script pasted below</option>
            <option value="system" >Use a different system executable such as sed</option>
        </param>
        <when value="Executable">
            <param name="exe_package" type="text" value="" label="Executable/package name for Ddependency manager - 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="text" value="" label="Command line override prefix - e.g. for sed or awk, prepend this before the i/o parameters" 
             help="This may help finesse a command line - inputs and output will be passed as you specify below"/>
        </when>
        <when value = "python">
           <expand macro="dynpar" />
        </when>
        <when value = "r-base">
           <expand macro="dynpar" />
        </when>
        <when value = "perl">
           <expand macro="dynpar" />
        </when>
        <when value = "bash">
           <expand macro="builtin_dynpar" />
        </when>
        <when value = "sh">
           <expand macro="builtin_dynpar" />
        </when>
    </conditional>
    <conditional name = "ppass">

        <param name="parampass"  type="select" display="radio" label="Command line parameter passing method to use">
            <option value="argparse" selected="true">Argparse style: passed in the form of '--[clname] [value]'</option>
            <option value="positional">Positional: Passed in the order of positional ordinals '...foo.bam bar.idx zot.xls'</option>
            <option value="0">No parameters needed because tool reads selected input file from STDIN and writes STDOUT with new history output"</option>
        </param>
        <when value = "argparse">
            <expand macro="io" />
            <expand macro="additparam" />
        </when>
        <when value = "positional">
            <expand macro="io" />
            <expand macro="additparam" />
        </when>
        <when value = "0">
             <expand macro="io"/>
        </when>
    </conditional>
    <conditional name="makeMode">
        <param name="make_Tool" type="select" display="radio" label="Generate new tool as  a tar.gz file ready to upload to a toolshed repository"
          help="Generate a toolshed archive - upload to a toolshed from where it can be auto-installed via the Galaxy admin functions" >
        <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
        <option value="" selected="true">No. Just run the script please</option>
        </param>
        <when value = "yes">
            <param name="planemo_test" type="select" display="radio" label="Use planemo to test the new tool (takes a while..)"
              help="Planemo will test the tool, upload it to the local toolshed and install to this Galaxy for additional testing" >
            <option value="yes" selected="true">Test with planemo and install to this Galaxy if passes</option>
            <option value="">No test/install</option>
            </param>
            <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
            <param name="tool_desc" label="Tool Description" type="text" value=""
             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
            value="**What it Does**"
             help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
                <sanitizer>
                    <valid initial="string.printable">
                    </valid>
                    <mapping initial="none"/>
                </sanitizer>

                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </repeat>
        </when>
        <when value = "">
        </when>
    </conditional>
  </inputs>
  <outputs>

    <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" >
        <filter>makeMode['make_Tool'] == "yes"</filter>
    </data>

  <collection name="TF_run_report" type="list" label="${tool_name} outputs">
      <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
  </collection>

    <param name="input_formats" value="txt" />
    <param name="input_label" value="input" />
    <param name="input_help" value="help" />
    <param name="tool_name" value="pyrevpos" />
    <param name="parampass" value="positional" />
    <param name="make_Tool" value="yes" />
    <param name="tool_version" value="0.01" />
    <param name="tool_desc" value="positional reverse" />
    <param name="help_text" value="help text goes here" />
    <param name="interpreter" value="python"/>
    <param name="history_name" value="output2_sample" />

49:35a912ce0c83

<tool id="rgTF2" name="toolfactory" version="2.00" profile="16.04" >
  <description>Scripts into tools</description>
  <macros>
     <xml name="planemo_steps">
         <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
            help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
            <param name="tool_desc" label="Tool Description" type="text" value=""
             help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
            <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
            value="**What it Does**"
             help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
                <sanitizer>
                    <valid initial="string.printable">
                    </valid>
                    <mapping initial="none"/>
                </sanitizer>

                            </sanitizer>
                        </param>
                    </when>
                </conditional>
            </repeat>
     </xml>
     <xml name="io">
        <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed"
             help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool">
            <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false"
               help=""/>
            <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
              help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
               <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
                <column name="value" index="0"/>
               </options>
            </param>
            <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative"
             help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
            </param>
            <param name="input_help" type="text" value="parameter_help" label="This will become help text on the form."
             help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation">
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
            </param>
            <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
              help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value="">
            </param>
        </repeat>
        <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed"
             help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
            <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help=""/>
            <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
              help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
               <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
                <column name="value" index="0"/>
               </options>
            </param>
            <param name="history_CL" type="text"  label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required."
              help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/>
            <param name="history_test" type="text"  label="Test pass decision criterion for this output compared to test generation"
              help="Available options are diff:lines, sim_size" value="diff:2"/>
        </repeat>
     </xml>
     <xml name="additparam">
        <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?"
             help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
            <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
            <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
        </param>

        <repeat name="additional_parameters" title="Pass additional parameters to the script"
             help="See examples below to see how these can be parsed by scripts in the various languages">
          <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter">
            <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"/>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_type" type="select" label="Select the type for this parameter">
            <option value="text" selected="true">text</option>
            <option value="integer">integer</option>
            <option value="float">float</option>
          </param>
          <param name="param_value" type="text" value="" label="Enter this parameter's default value"
            help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form"
             help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_help" type="text" value="parameter_help" label="Help for this parameter"
             help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" >
            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </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"
              help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
        </repeat>
     </xml>
  </macros>
  <requirements>
      <requirement type="package">python</requirement>
      <requirement type="package">perl</requirement>
      <requirement type="package">r-base</requirement>
      <requirement type="package">galaxyxml</requirement>
      <requirement type="package">planemo</requirement>
      <requirement type="package">yaml</requirement>
      <requirement type="package">lxml</requirement>
  </requirements>
  <command interpreter="python"><![CDATA[
#import os
#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:
$__tool_directory__/rgToolFactory2.py
    #if len(str($cl_prefix)) > 3:
--cl_prefix "$cl_prefix"
    #end if
    #if $cover.commover == "yes":
       #if len(str($cover.command_override)) > 10:
--command_override "$commandoverride"
       #end if
       #if len(str($cover.test_override)) > 10:
--test_override "$testoverride"
       #end if
    #end if
    #if $interexe.dependency_model == "managed":
--packages "$interexe.packages"
    #else:
--sysexe "$interexe.sysexe"
    #end if
--tool_name="$tool_name"  --user_email="$__user_email__" --citations="$citeme"  --parampass="$ppass.parampass"
   #if $usescript.choosescript == "yes":
--script_path "$runme"
   #end if
   #if str($makeMode.make_Tool)!="runonly":
--make_Tool="$makeMode.make_Tool"
--tool_desc="$makeMode.tool_desc"
--tool_version="$makeMode.tool_version"
--help_text="$helpme"
--new_tool="$new_tool"
   #end if
   #if $ppass.parampass != '0':
     #if str($ppass.edit_params) == "yes":
--edit_additional_parameters
     #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~~~$otab.history_test"
     #end for
 #end if
]]></command>
 <configfiles>
  <configfile name="runme">
#if $usescript.choosescript == 'yes':
$usescript.dynScript
#end if
 </configfile>
 <configfile name="commandoverride">
#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
$cover.command_override
#end if
 </configfile> 
 <configfile name="testoverride">
#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
$cover.test_override
#end if
 </configfile> 
 <configfile name="helpme">
    #if $makeMode.make_Tool != "runonly":
${makeMode.help_text}
    #else
$tool_name help goes here
    #end if
 </configfile>
 <configfile name="citeme">
#if $makeMode.make_Tool != "runonly":
    #for $citation in $makeMode.citations:
        #if $citation.citation_type.type == "bibtex":
            **ENTRY**bibtex
            ${citation.citation_type.bibtex}
        #else
            **ENTRY**doi
            ${citation.citation_type.doi}
        #end if
    #end for
#end if
 </configfile>
  </configfiles>
  <inputs>
   <param name="tool_name" type="text" value="tool1"   label="New tool ID and title for outputs"
         help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits">
                <add value="_"/>
            </valid>
        </sanitizer>
    </param>
  
    <conditional name="interexe">
        <param name="dependency_model" type="select" label="Dependency model: Conda managed external dependency or existing system executable"
        help = "If managed, the supplied package will become a requirement so must match the tool dependency resolver package name in conda.">
            <option value="managed" selected="true" >Use Conda managed dependencies</option>
            <option value="system" >Use a non-dependency managed system executable like bash or awk</option>
        </param>
        <when value="managed">
            <param name="packages" type="text" value="" label="Package name[:version, name:version...] for Conda. First will be called on generated command line" optional="false"
             help="Use colon to append specific versiion like 'bwa:0.17.0'. Default is latest if no version. Will be used every time the tool is (re)run." /> 
            <param name="sysexe" type="hidden" value="" />
        </when>
       <when value="system">
            <param name="sysexe" type="text" value="" label="System executable to run. Supplied/managed by the operating system - not Conda" optional="false"
            help=".e.g bash, awk or other standard and relatively invariant unix utilities"/>
            <param name="packages" type="hidden" value="" />
        </when>
    </conditional>
    <conditional name="usescript">
        <param name="choosescript" type="select" display="radio" label="Choose whether to run a supplied script - useful only if the dependency can use them"
        help = "Useful for script interpreters like Python or bash. All i/o and parameters must be passed. Choose No unless script is needed.">
            <option value="no" selected="true">No script required for the first dependency above - just parameters on the command line</option>
            <option value="yes">A script is ready to be pasted below.</option>
        </param> 
        <when value="no">
            <param name="dynScript" type="hidden"  value="" />
        </when>
        <when value="yes">
            <param name="dynScript" type="text" area="True" value="" label="Script for first dependency to interpret. "
             help="Script must handle all i/o and parameters as specified below using the parameter passing method chosen above">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
             </param>
        </when>
    </conditional>
    <conditional name="ppass">
        <param name="parampass"  type="select" display="radio" label="Command line parameter passing method to use">
            <option value="argparse" selected="true">Argparse style: passed in the form of --clname value</option>
            <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
            <option value="0">Tool reads selected input file from STDIN and writes STDOUT with new history output with no parameters</option>
        </param>
        <when value="argparse">
            <expand macro="io" />
            <expand macro="additparam" />
        </when>
        <when value="positional">
            <expand macro="io" />
            <expand macro="additparam" />
        </when>
        <when value="0">
             <expand macro="io"/>
        </when>
    </conditional>
    <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely"
            help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." />
    <conditional name="cover">
        <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY"
        help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart">
            <option value="no" selected="true">Use automatically generated command/test XML </option>
            <option value="yes">DIY XML needed to replace autogenerated command and/or test segments will be pasted below</option>
        </param> 
        <when value="no">
            <param name="command_override" type="hidden"  value="" />
            <param name="test_override" type="hidden"  value="" />
        </when>
        <when value="yes">
            <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
             help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
             </param>
            <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
             help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param> 
        </when>
    </conditional>

    <conditional name="makeMode">
        <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. Docker is recommended if you want local installation"
          help="Testing and installation in this Galaxy is optional. Planemo run must be used if you are providing XML overrides for the command or test sections" >
        <option value="runonly">Run this configuration. NOT suitable for Executable command/test overriden tools</option>
        <option value="generate" selected="true">Run and generate toolshed archive containing the new tool. NOT suitable for command/test overriden tools</option>
        <option value="gentest">Run, generate and test the new tool with planemo. NOT suitable for command/test overriden tools</option>
        <option value="gentestinstall">Run, generate, planemo test and install (via the local toolshed) the new tool. NOT suitable for command/test overriden tools</option>
        <option value="planemogenerate">Planemo test twice - once to generate test outputs. Suitable for tools with or without command/test overrides but takes time</option>
        <option value="planemogeninstall">Planemo test twice and install. Suitable for tools with or without command/test overrides.</option>
        </param>
        <when value="runonly"/>
        <when value="generate">
            <expand macro="planemo_steps" />
        </when>
        <when value="gentest">
            <expand macro="planemo_steps" />
        </when>
       <when value="gentestinstall">
            <expand macro="planemo_steps" />
        </when>
        <when value="planemogenerate">
            <expand macro="planemo_steps" />
        </when>
        <when value="planemogeninstall">
            <expand macro="planemo_steps" />
        </when>
    </conditional>

  </inputs>
  <outputs>

    <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" >
        <filter>makeMode['make_Tool'] != "runonly"</filter>
    </data>

  <collection name="TF_run_report" type="list" label="${tool_name} outputs">
      <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
  </collection>

    <param name="input_formats" value="txt" />
    <param name="input_label" value="input" />
    <param name="input_help" value="help" />
    <param name="tool_name" value="pyrevpos" />
    <param name="parampass" value="positional" />
    <param name="make_Tool" value="generate" />
    <param name="tool_version" value="0.01" />
    <param name="tool_desc" value="positional reverse" />
    <param name="help_text" value="help text goes here" />
    <param name="interpreter" value="python"/>
    <param name="history_name" value="output2_sample" />