Mercurial > repos > fubar > toolfactory_gtn

comparison toolfactory/rgToolFactory2.xml @ 3:c4f192ec521c draft

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author fubar
date Tue, 20 Apr 2021 05:30:52 +0000
parents b65ec4f387b9
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2:b65ec4f387b9 3:c4f192ec521c
62 </conditional> 62 </conditional>
63 </repeat> 63 </repeat>
64 </xml> 64 </xml>
65 <xml name="io"> 65 <xml name="io">
66 <section name="io" title="Input and output files" expanded="true"> 66 <section name="io" title="Input and output files" expanded="true">
67 <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable." 67 <repeat name="history_inputs" title="Inputs" min="0"
68 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"> 68 help="Input data files to pass on the command line to the executable. USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool">
69 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false" 69 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false"
70 help=""/> 70 help=""/>
71 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" 71 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
72 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> 72 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
73 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 73 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
81 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it" 81 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
82 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=""> 82 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="">
83 </param> 83 </param>
84 <param name="input_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as wanted - script/executable must parse these."/> 84 <param name="input_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as wanted - script/executable must parse these."/>
85 </repeat> 85 </repeat>
86 <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" 86 <repeat name="history_outputs" min="1" title="Outputs"
87 help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> 87 help="New history items output by the executable to appear in the user history after the tool runs. The name will become a history item for users of the new tool you are making containing one of it's outputs">
88 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" 88 <param name="history_name" type="text" label="Output Name" optional="false"
89 help="No spaces! Argparse will also use this name as --[name]"> 89 help="Name used for this output in history. No spaces! Argparse will also use this name as --[name]">
90 <sanitizer invalid_char="_"> 90 <sanitizer invalid_char="_">
91 <valid initial="string.ascii_letters,string.digits" > 91 <valid initial="string.ascii_letters,string.digits" >
92 <add value="_" /> 92 <add value="_" />
93 </valid> 93 </valid>
94 </sanitizer> 94 </sanitizer>
97 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> 97 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
98 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 98 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
99 <column name="value" index="0"/> 99 <column name="value" index="0"/>
100 </options> 100 </options>
101 </param> 101 </param>
102 <param name="history_CL" type="text" label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used" 102 <param name="history_CL" type="text" label="Position"
103 help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> 103 help="Positional: ordinal integer or 'STDOUT' if '>' required. Otherwise ignored if argparse because name is used. If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
104 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" 104 <param name="history_test" type="text" label="Output test criteria"
105 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> 105 help="Pass/fail decision criterion for this output compared to test generation. Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/>
106 </repeat> 106 </repeat>
107 <repeat name="collection_outputs" title="zero or more new history collections to appear in the user history after the tool runs" 107 <repeat name="collection_outputs" title="Output Collections" min="0"
108 help="Hides outputs not needed for downstream tools such as images and intermediate reports." default="0"> 108 help="New history collections to appear in the user history after the tool runs. Hides outputs not needed for downstream tools such as images and intermediate reports." default="0">
109 <param name="name" type="text" label="Name for new collection with all outputs not individually passed to history outputs" 109 <param name="name" type="text" label="Name"
110 help="No spaces! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints"> 110 help="for new collection with all outputs not individually passed to history outputs. No spaces! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints">
111 <sanitizer invalid_char="_"> 111 <sanitizer invalid_char="_">
112 <valid initial="string.ascii_letters,string.digits" > 112 <valid initial="string.ascii_letters,string.digits" >
113 <add value="_" /> 113 <add value="_" />
114 </valid> 114 </valid>
115 </sanitizer> 115 </sanitizer>
125 </repeat> 125 </repeat>
126 126
127 </section> 127 </section>
128 </xml> 128 </xml>
129 <xml name="additparam"> 129 <xml name="additparam">
130 <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true"> 130 <section name="addparam" title="Arguments" help="Executable or script settings passed on the command line other than I/O files" expanded="true">
131 <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?" 131 <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
132 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"> 132 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">
133 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option> 133 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
134 <option value="no">No - use the fixed values for all additional parameters - no user editing</option> 134 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
135 </param> 135 </param>
136 <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable" 136 <repeat name="additional_parameters" title="Command Line Paramters" min="0"
137 help="See examples below to see how these can be parsed by scripts in the various languages"> 137 help="Command line settings for the user to pass to the executable. See examples below to see how these can be parsed by scripts in the various languages">
138 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> 138 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
139 <sanitizer invalid_char=""> 139 <sanitizer invalid_char="">
140 <valid initial="string.ascii_letters,string.digits"/> 140 <valid initial="string.ascii_letters,string.digits"/>
141 <mapping initial="none"/> 141 <mapping initial="none"/>
142 </sanitizer> 142 </sanitizer>
180 </macros> 180 </macros>
181 181
182 <requirements> 182 <requirements>
183 <requirement type="package" version="0.4.14">galaxyxml</requirement> 183 <requirement type="package" version="0.4.14">galaxyxml</requirement>
184 <requirement type="package" version="0.74.3">planemo</requirement> 184 <requirement type="package" version="0.74.3">planemo</requirement>
185 <requirement type="package" version="0.10.6">ephemeris</requirement>
185 </requirements> 186 </requirements>
186 187
187 <command detect_errors="exit_code"><![CDATA[ 188 <command detect_errors="exit_code"><![CDATA[
188 #import os 189 #import os
189 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' 190 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'