Mercurial > repos > fubar > tool_factory_2

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

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author fubar
date Tue, 01 Dec 2020 09:03:34 +0000
parents 5509dc4c1cf2
children bf7b4b603bf9
comparison
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112:5509dc4c1cf2 113:6873c211b250
37 </when> 37 </when>
38 </conditional> 38 </conditional>
39 </repeat> 39 </repeat>
40 </xml> 40 </xml>
41 <xml name="io"> 41 <xml name="io">
42 <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed" 42 <repeat name="history_inputs" title="zero or more input data file parameters to appear on the tool form to be passed to the executable"
43 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"> 43 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">
44 <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" 44 <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false"
45 help=""/> 45 help=""/>
46 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" 46 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
47 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> 47 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
65 </param> 65 </param>
66 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" 66 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
67 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=""> 67 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="">
68 </param> 68 </param>
69 </repeat> 69 </repeat>
70 <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" 70 <repeat name="history_outputs" title="one or more output file parameters generated by the tool to be added to the user history"
71 help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> 71 help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
72 <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]"/> 72 <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]"/>
73 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" 73 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
74 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> 74 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
75 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 75 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
81 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" 81 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation"
82 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="sim_size:0.01"/> 82 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="sim_size:0.01"/>
83 </repeat> 83 </repeat>
84 </xml> 84 </xml>
85 <xml name="additparam"> 85 <xml name="additparam">
86 <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?" 86 <param name="edit_params" type="select" display="radio" label="Make parameters on the generated tool form user editable?"
87 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"> 87 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">
88 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option> 88 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
89 <option value="no">No - use the fixed values for all additional parameters - no user editing</option> 89 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
90 </param> 90 </param>
91 91
92 <repeat name="additional_parameters" title="Pass additional parameters to the script" 92 <repeat name="additional_parameters" title="zero or more user supplied parameter fields to the tool form for the executable"
93 help="See examples below to see how these can be parsed by scripts in the various languages"> 93 help="See examples below to see how these can be parsed by scripts in the various languages">
94 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> 94 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
95 <sanitizer invalid_char=""> 95 <sanitizer invalid_char="">
96 <valid initial="string.letters,string.digits"/> 96 <valid initial="string.letters,string.digits"/>
97 <mapping initial="none"/> 97 <mapping initial="none"/>
236 <add value="_"/> 236 <add value="_"/>
237 </valid> 237 </valid>
238 </sanitizer> 238 </sanitizer>
239 </param> 239 </param>
240 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes" 240 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
241 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" /> 241 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" />
242 242
243 <conditional name="usescript"> 243 <conditional name="usescript">
244 <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" 244 <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"
245 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"> 245 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">
246 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> 246 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>