comparison toolfactory/rgToolFactory2.xml @ 63:b3254219d4fb draft

Uploaded

62:881bd8c81ac9

<tool id="rgtf2" name="toolfactory" version="2.01" profile="16.04" >
  <description>Scripts into tools v2.0</description>
  <macros>
     <xml name="tool_metadata">
         <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"/>

            <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>

        </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>

            <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>

  </macros>

<requirements>
       <requirement type="package" version="0.72.0" >planemo</requirement>
       <requirement type="package" version="0.4.11" >galaxyxml</requirement>
</requirements>
  
  <command ><![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__ ):
python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__

       #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

--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~~~$otab.history_test"
     #end for
--galaxy_root="$__root_dir__"
 #end if
]]></command>
 <configfiles>
  <configfile name="runme">
$usescript.dynScript
 </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

            <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 for scripting (python, R,....) or command line packages (bwa,samtools)</option>
            <option value="system" >Use a non-dependency managed system executable for scripting like bash or command line driven like sed or awk</option>
        </param>
        <when value="managed">
            <param name="packages" type="text" value="" label="Package name[:version, name:version...] for Conda. First (e.g. python) will be called on generated command line" 
            optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. 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. OS version - not Conda managed" 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="Run a supplied script if the dependency reads one (e.g. python/R/bash)"
        help = "For script interpreters like Python or bash. Parameters and i/o below must match script's expectations">
            <option value="no" selected="true">No script required for the first dependency above - just parameters on the command line</option>
            <option value="yes">Yes, a script is ready to be pasted below for the chosen package</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 above (e.g. python) to interpret. "
             help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
              <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: 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 no parameters</option>

    <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">No. Use automatically generated command/test XML </option>
            <option value="yes">Yes. XML needed to override 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">

              <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. The TF Docker container is recommended for local installation"
          help="Testing and installation in this Galaxy are optional" >
        <option value="runonly">Run this configuration in Galaxy (will run Planemo if command or test override in play)</option>
        <option value="generate">Generate a toolshed ready archive.</option>
        <option value="gentest" selected="true">Test with planemo after generating.</option>
        <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
        </param>
        <when value="runonly"/>
        <when value="generate">
            <expand macro="tool_metadata" />
        </when>
       <when value="gentest">
            <expand macro="tool_metadata" />
        </when>
       <when value="gentestinstall">
            <expand macro="tool_metadata" />
        </when>
    </conditional>

  </inputs>

    <param name="history_CL" value="2" />
    <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
    <param name="choosescript" value="yes" />
    <param name="script_path" value="$runme"/>
    <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
</test>
</tests>
<help>

.. class:: warningmark

      o.write('\n')
    o.close()



Paper_ 

*Licensing*

Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
All rights reserved.

63:b3254219d4fb

<tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
  <description>Scripts into tools v2.0</description>
  <macros>
     <xml name="tool_metadata">
         <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"/>

            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
            </param>
            <param name="input_help" type="text" value="" 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>

        </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" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
            <option value="no">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="" label="Choose the name for this parameter - MUST not be blank!">
            <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"/>
              <mapping initial="none"/>
            </sanitizer>
          </param>

            <sanitizer invalid_char="">
              <valid initial="string.printable"> <remove value='~~~'/> </valid>
              <mapping initial="none"/>
            </sanitizer>
          </param>
          <param name="param_label" type="text" value="" 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="" 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>

  </macros>

<requirements>
       <requirement type="package" version="0.72.0" >planemo</requirement>
       <requirement type="package" version="0.4.11" >galaxyxml</requirement>

</requirements>

  <command ><![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__ ):
python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__

       #end if
       #if len(str($cover.test_override)) > 10:
--test_override "$testoverride"
       #end if
    #end if
--packages "$packages"
   #if $usescript.choosescript == "yes":
--script_path "$runme"
--sysexe "$usescript.scriptrunner"
    #end if
--tool_name="$tool_name"  --user_email="$__user_email__" --citations="$citeme"  --parampass="$ppass.parampass"

   #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"
--toolshed_api_key="$makeMode.toolshed_apikey"
--galaxy_api_key="$makeMode.galaxy_apikey"
--toolshed_url="$makeMode.toolshed_url"
--galaxy_url="$makeMode.galaxy_url"
   #end if
   #if $ppass.parampass != '0':
     #if str($ppass.edit_params) == "yes":
--edit_additional_parameters
     #end if

--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~~~$otab.history_test"
     #end for
--galaxy_root "$__root_dir__"
 #end if
]]></command>
 <configfiles>
  <configfile name="runme">
$usescript.dynScript
 </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

            <valid initial="string.letters,string.digits">
                <add value="_"/>
            </valid>
        </sanitizer>
    </param>
    <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
    optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported"  />

    <conditional name="usescript">
        <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash"
        help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them">
            <option value="no" selected="true">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
            <option value="yes">Yes, a script is ready to be pasted below</option>
        </param>
        <when value="no">
            <param name="dynScript" type="hidden"  value="" />
            <param name="scriptrunner" type="hidden"  value="" />
        </when>
        <when value="yes">
            <param name="scriptrunner" type="text" value=""   label="Interpreter for the script pasted below - 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">
                    <add value="_"/>
                </valid>
            </sanitizer>
            </param>
            <param name="dynScript" type="text" area="True" value="" label="Script for executable below to interpret. It can be one of the Conda dependency names "
             help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
              <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: 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 no parameters</option>

    <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">No. Use automatically generated command/test XML </option>
            <option value="yes">Yes. XML needed to override 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">

              <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. The TF Docker container is recommended for local installation"
          help="Installation in this Galaxy is optional" >
        <option value="gentest" selected="true">Test with planemo after generating.</option>
        <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
        </param>
       <when value="gentest">
           <param name="galaxy_apikey" value="" type="hidden"  ></param>
           <param name="toolshed_apikey" value="" type="hidden"  ></param>
           <param name="galaxy_url" value="" type="hidden"  ></param>
           <param name="toolshed_url" value="" type="hidden"  ></param>
            <expand macro="tool_metadata" />
        </when>
       <when value="gentestinstall">
            <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed"
             help="Default is localhost">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param>
          <param name="galaxy_apikey" type="text" value="" label="API key for the Galaxy to install the new tool"
             help="Cut and paste from the admin user properties screen">
              <sanitizer>
                 <valid initial="string.letters,string.digits">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param>
           <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed"
             help="Default value is localhost:9009">
              <sanitizer>
                 <valid initial="string.printable">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param>
           <param name="toolshed_apikey" type="text" value="" label="API key for the local toolshed to use when installing the tool"
             help="Cut and paste from the admin user properties screen">
              <sanitizer>
                 <valid initial="string.letters,string.digits">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param>

            <expand macro="tool_metadata" />
        </when>
    </conditional>

  </inputs>

    <param name="history_CL" value="2" />
    <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
    <param name="choosescript" value="yes" />
    <param name="script_path" value="$runme"/>
    <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />

</test>
</tests>
<help>

.. class:: warningmark

      o.write('\n')
    o.close()



Paper_

*Licensing*

Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
All rights reserved.