comparison toolfactory/rgToolFactory2.xml @ 113:6873c211b250 draft

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112:5509dc4c1cf2

                    </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">

            </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="Argparse will also use this name as --[name]"/>
            <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">

            <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="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"/>

                <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 for 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">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>

113:6873c211b250

                    </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="Argparse will also use this name as --[name]"/>
            <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">

            <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"/>

                <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"
        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">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>