comparison toolfactory/rgToolFactory2.xml @ 118:e43c43396a70 draft

Uploaded

117:b1a29d3d50d6

<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"/>
            <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">

                    </when>
                </conditional>
            </repeat>
     </xml>
     <xml name="io">
        <repeat name="history_inputs" title="zero or more input data file parameters to appear on the tool form to be passed to the executable"
             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">

            </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="one or more output file parameters generated by the tool to be added to the user history"
             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="No spaces! Argparse will also use this name as --[name]">
              <sanitizer invalid_char="_">
                <valid initial="string.letters,string.digits"/>

               </options>
            </param>
            <param name="history_CL" type="text"  label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used"
              help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" 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:[delta (integer) or delta_frac (float)" value="sim_size:0.01"/>
        </repeat>
     </xml>
     <xml name="additparam">
        <param name="edit_params" type="select" display="radio" label="Make parameters on the generated tool form 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="zero or more user supplied parameter fields to the tool form for the executable"
             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"/>

          <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" 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> -->
  <container type="docker">quay.io/fubar2/planemo-biocontainer:latest</container>
</requirements>

  <command ><![CDATA[
#import os
#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'

       #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
     #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~~~$otab.history_test"
     #end for
--galaxy_root "$__root_dir__"
--tool_dir "$__tool_directory__"
 #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

#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

            <valid initial="string.ascii_lowercase,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] or :[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 for a dependency (e.g. python/R/bash) or a system executable such as Bash"

                 <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>

        </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">

                 <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="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
        <option value="gentest">Test with planemo after generating.</option>

                 <valid initial="string.letters,string.digits">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param>

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

  </inputs>
  <outputs>

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

118:e43c43396a70

<tool id="rgtfd" 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"/>
            <param name="tool_desc" label="Tool Synopsis" type="text" value=""
             help="Supply a brief tool description for the Galaxy tool menu entry" />
            <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">

                    </when>
                </conditional>
            </repeat>
     </xml>
     <xml name="io">
     <section name="io" title="Input and output files" expanded="true">
        <repeat name="history_inputs" title="zero or more input data files to pass as parameters to the executable."
             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">

            </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="one or more new history items output by the executable to appear in the user history after the tool runs"
             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="No spaces! Argparse will also use this name as --[name]">
              <sanitizer invalid_char="_">
                <valid initial="string.letters,string.digits"/>

               </options>
            </param>
            <param name="history_CL" type="text"  label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used"
              help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" 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:[delta (integer) or delta_frac (float)" value="diff:0"/>
        </repeat>
        </section>
     </xml>
     <xml name="additparam">
     <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true">
        <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
             help="If no, 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="zero or more settings to be set by the tool user and passed on the command line"
             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"/>

          <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>
        </section>
     </xml>
  </macros>

<requirements>
   <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>
</requirements>

  <command ><![CDATA[
#import os
#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'

       #end if
       #if len(str($cover.test_override)) > 10:
--test_override "$testoverride"
       #end if
    #end if
--packages "$deps.packages"
   #if $deps.usescript.choosescript == "yes":
--script_path "$runme"
--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 "$make.makeMode.tool_desc"
--tool_version "$make.makeMode.tool_version"
--help_text "$helpme"
--new_tool "$new_tool"
--toolshed_api_key "$make.makeMode.toolshed_apikey"
--galaxy_api_key "$make.makeMode.galaxy_apikey"
--toolshed_url "$make.makeMode.toolshed_url"
--galaxy_url "$make.makeMode.galaxy_url"
   #end if
   #if $io_param.ppass.parampass != '0':
     #if str($io_param.ppass.addparam.edit_params) == "yes":
--edit_additional_parameters
     #end if
     #for apar in $io_param.ppass.addparam.additional_parameters:
--additional_parameters "$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 $io_param.ppass.io.history_inputs:
--input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
     #end for
     #for $otab in $io_param.ppass.io.history_outputs:
--output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
     #end for
--galaxy_root "$__root_dir__"
--tool_dir "$__tool_directory__"
 #end if
]]></command>
 <configfiles>
  <configfile name="runme">
$deps.usescript.dynScript
 </configfile>
 <configfile name="commandoverride">
#if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
$cover.command_override
#end if

#if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
$cover.test_override
#end if
 </configfile>
 <configfile name="helpme">
    #if $make.makeMode.make_Tool != "runonly":
${make.makeMode.help_text}
    #else
$tool_name help goes here
    #end if
 </configfile>
 <configfile name="citeme">
#if $make.makeMode.make_Tool != "runonly":
    #for $citation in $make.makeMode.citations:
        #if $citation.citation_type.type == "bibtex":
            **ENTRY**bibtex
            ${citation.citation_type.bibtex}
        #else
            **ENTRY**doi

            <valid initial="string.ascii_lowercase,string.digits">
                <add value="_"/>
            </valid>
        </sanitizer>
    </param>

    <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">

    <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] or :[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 for a dependency (e.g. python/R/bash) or a system executable such as Bash"

                 <mapping initial="none"/>
              </sanitizer>
             </param>
        </when>
    </conditional>
    </section>
    <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
    <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>

        </when>
        <when value="0">
             <expand macro="io"/>
        </when>
    </conditional>
    </section>
    <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">

                 <mapping initial="none"/>
              </sanitizer>
            </param>
        </when>
    </conditional>
     <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
    <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="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
        <option value="gentest">Test with planemo after generating.</option>

                 <valid initial="string.letters,string.digits">
                 </valid>
                 <mapping initial="none"/>
              </sanitizer>
            </param>
            <expand macro="tool_metadata" />
        </when>
    </conditional>
    </section>
  </inputs>
  <outputs>

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