comparison toolfactory/rgToolFactory2.xml @ 112:5509dc4c1cf2 draft

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111:223b78754735

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

112:5509dc4c1cf2

    </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>
            <option value="yes" selected="true">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 - 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 above 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"/>