Mercurial > repos > fubar > tool_factory_docker

comparison toolfactory_docker/rgToolFactory2.xml @ 6:482386d6cc43 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Sun, 24 Jan 2021 03:54:01 +0000
parents b4985006fb05
children
comparison
equal deleted inserted replaced
5:f17a2b1972f1 6:482386d6cc43
1 <tool id="rgtfd" name="toolfactory" version="2.00" profile="16.04" > 1 <tool id="rgtfd" name="toolfactory" version="2.00" profile="16.04" >
2 <description>Scripts into tools v2.0</description> 2 <description>Scripts into tools v2.0</description>
3 <macros> 3 <macros>
4 <xml name="singleText">
5 <param name="param_value" type="text" value="" label="Enter this parameter's default text value">
6 </param>
7 </xml>
8 <xml name="singleInt">
9 <param name="param_value" type="integer" value="" label="Enter this parameter's default integer value" >
10 </param>
11 </xml>
12 <xml name="singleFloat">
13 <param name="param_value" type="float" value="" label="Enter this parameter's default value">
14 </param>
15 </xml>
16 <xml name="singleBoolean">
17 <param name="param_value" type="boolean" value="" label="Enter this parameter's default value" />
18 <param name="truevalue" type="text" value="True" label="Command line value to emit when True" />
19 <param name="falsevalue" type="boolean" value="True" label="Command line value to emit when False" />
20 </xml>
21 <xml name="selectText">
22 <repeat name="selectTexts" title="Add each option to be presented in a text select box" min="2" default="2"
23 help="Each text added here will also have a value to be emitted on the command line when the text is chosen">
24 <param name="select_text" type="text" value="" label="Enter the explanatory text the user will see for this choice" >
25 </param>
26 <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
27 </param>
28 </repeat>
29 </xml>
4 <xml name="tool_metadata"> 30 <xml name="tool_metadata">
5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" 31 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
6 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> 32 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
7 <param name="tool_desc" label="Tool Synopsis" type="text" value="" 33 <param name="tool_desc" label="Tool Synopsis" type="text" value=""
8 help="Supply a brief tool description for the Galaxy tool menu entry" /> 34 help="Supply a brief tool description for the Galaxy tool menu entry" />
36 </conditional> 62 </conditional>
37 </repeat> 63 </repeat>
38 </xml> 64 </xml>
39 <xml name="io"> 65 <xml name="io">
40 <section name="io" title="Input and output files" expanded="true"> 66 <section name="io" title="Input and output files" expanded="true">
41 <repeat name="history_inputs" title="zero or more input data files to pass as parameters to the executable." 67 <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable."
42 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="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 <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false" 69 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false"
44 help=""/> 70 help=""/>
45 <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"
46 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">
47 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 73 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
48 <column name="value" index="0"/> 74 <column name="value" index="0"/>
49 </options> 75 </options>
50 </param> 76 </param>
51 <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" 77 <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" >
52 help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > 78 </param>
53 <sanitizer invalid_char=""> 79 <param name="input_help" type="text" value="" label="This will become help text on the form." >
54 <valid initial="string.printable">
55 <remove value='~~~' />
56 </valid>
57 <mapping initial="none"/>
58 </sanitizer>
59 </param>
60 <param name="input_help" type="text" value="" label="This will become help text on the form."
61 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation">
62 <sanitizer invalid_char="">
63 <valid initial="string.printable">
64 <remove value='~~~' />
65 </valid>
66 <mapping initial="none"/>
67 </sanitizer>
68 </param> 80 </param>
69 <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"
70 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="">
71 </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 needed." />
72 </repeat> 85 </repeat>
73 <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" title="one or more new history items output by the executable to appear in the user history after the tool runs"
74 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="The name will become a history item for users of the new tool you are making containing one of it's outputs">
75 <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="Name for this output to appear in new history" optional="false"
76 help="No spaces! Argparse will also use this name as --[name]"> 89 help="No spaces! Argparse will also use this name as --[name]">
89 <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="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used"
90 help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> 103 help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
91 <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="Test pass decision criterion for this output compared to test generation"
92 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> 105 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/>
93 </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"
108 help="A collection contains 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"
110 help="No spaces! ">
111 <sanitizer invalid_char="_">
112 <valid initial="string.ascii_letters,string.digits" >
113 <add value="_" />
114 </valid>
115 </sanitizer>
116 </param>
117 <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output"
118 help="">
119 <option value="list" selected="true">List</option>
120 <option value="paired">Paired</option>
121 <option value="list:paired">List of paired</option>
122 </param>
123 <param name="label" type="text" label="Label for this collection" help="" value=""/>
124 <param name="discover" type="text" label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions" value="__name_and_ext__"/>
125 </repeat>
126
94 </section> 127 </section>
95 </xml> 128 </xml>
96 <xml name="additparam"> 129 <xml name="additparam">
97 <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="Executable or script settings passed on the command line other than I/O files" expanded="true">
98 <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?"
99 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">
100 <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>
101 <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>
102 </param> 135 </param>
103 136 <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable"
104 <repeat name="additional_parameters" title="zero or more settings to be set by the tool user and passed on the command line"
105 help="See examples below to see how these can be parsed by scripts in the various languages"> 137 help="See examples below to see how these can be parsed by scripts in the various languages">
106 <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!">
107 <sanitizer invalid_char=""> 139 <sanitizer invalid_char="">
108 <valid initial="string.ascii_letters,string.digits"/> 140 <valid initial="string.ascii_letters,string.digits"/>
109 <mapping initial="none"/> 141 <mapping initial="none"/>
110 </sanitizer> 142 </sanitizer>
111 </param> 143 </param>
144 <conditional name="ap_type">
112 <param name="param_type" type="select" label="Select the type for this parameter"> 145 <param name="param_type" type="select" label="Select the type for this parameter">
113 <option value="text" selected="true">text</option> 146 <option value="text" selected="true">Text string</option>
114 <option value="integer">integer</option> 147 <option value="integer">Integer</option>
115 <option value="float">float</option> 148 <option value="float">Float</option>
116 </param> 149 <option value="boolean">Boolean</option>
117 <param name="param_value" type="text" value="" label="Enter this parameter's default value" 150 <option value="selecttext">Select text string</option>
118 help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" > 151 </param>
119 <sanitizer invalid_char=""> 152 <when value = "text">
120 <valid initial="string.printable"> 153 <expand macro="singleText" />
121 <remove value='~~~' /> 154 </when>
122 </valid> 155 <when value = "integer">
123 <mapping initial="none"/> 156 <expand macro="singleInt" />
124 </sanitizer> 157 </when>
125 </param> 158 <when value = "float">
126 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form" 159 <expand macro="singleFloat" />
127 help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > 160 </when>
128 <sanitizer invalid_char=""> 161 <when value = "boolean">
129 <valid initial="string.printable"> 162 <expand macro="singleBoolean" />
130 <remove value='~~~'/> 163 </when>
131 </valid> 164 <when value = "selecttext">
132 <mapping initial="none"/> 165 <expand macro="selectText" />
133 </sanitizer> 166 </when>
134 </param> 167 </conditional>
135 <param name="param_help" type="text" value="" label="Help for this parameter" 168 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form">
136 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" > 169 </param>
137 <sanitizer invalid_char=""> 170 <param name="param_help" type="text" value="" label="Help for this parameter">
138 <valid initial="string.printable">
139 <remove value='~~~'/>
140 </valid>
141 <mapping initial="none"/>
142 </sanitizer>
143 </param> 171 </param>
144 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name" 172 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
145 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="" /> 173 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="" />
146 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" 174 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
147 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> 175 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
196 #end if 224 #end if
197 #if $io_param.ppass.parampass != '0': 225 #if $io_param.ppass.parampass != '0':
198 #if str($io_param.ppass.addparam.edit_params) == "yes": 226 #if str($io_param.ppass.addparam.edit_params) == "yes":
199 --edit_additional_parameters 227 --edit_additional_parameters
200 #end if 228 #end if
201 #for apar in $io_param.ppass.addparam.additional_parameters: 229 #for $apar in $io_param.ppass.addparam.additional_parameters:
202 --additional_parameters "$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed" 230 #if $apar.ap_type.param_type=="selecttext":
231 --selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
232 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
233 #for $i,$st in enumerate($apar.ap_type.selectTexts):
234 "$st.select_value"
235 #if ($i < (len($apar.ap_type.selectTexts)-1)):
236 ,
237 #end if
238 #end for
239 ], "texts": [
240 #for $i,$st in enumerate($apar.ap_type.selectTexts):
241 "$st.select_text"
242 #if ($i < (len($apar.ap_type.selectTexts)-1)):
243 ,
244 #end if
245
246 #end for
247 ]
248 }'
249 #else:
250 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
251 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed" }'
252 #end if
203 #end for 253 #end for
204 #end if 254 #end if
205 #for $intab in $io_param.ppass.io.history_inputs: 255 #for $intab in $io_param.ppass.io.history_inputs:
206 --input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" 256 --input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}'
207 #end for 257 #end for
208 #for $otab in $io_param.ppass.io.history_outputs: 258 #for $otab in $io_param.ppass.io.history_outputs:
209 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" 259 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'
260 #end for
261 #for $collect in $io_param.ppass.io.collection_outputs:
262 --collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
210 #end for 263 #end for
211 --galaxy_root "$__root_dir__" 264 --galaxy_root "$__root_dir__"
212 --tool_dir "$__tool_directory__" 265 --tool_dir "$__tool_directory__"
213 #end if 266 #end if
214 ]]></command> 267 ]]></command>
258 </param> 311 </param>
259 312
260 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true"> 313 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
261 314
262 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes" 315 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
263 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" /> 316 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" />
264 317
265 <conditional name="usescript"> 318 <conditional name="usescript">
266 <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" 319 <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"
267 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"> 320 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">
268 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> 321 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
343 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true"> 396 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
344 <conditional name="makeMode"> 397 <conditional name="makeMode">
345 <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" 398 <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"
346 help="Installation in this Galaxy is optional" > 399 help="Installation in this Galaxy is optional" >
347 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> 400 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
348 <option value="gentest">Test with planemo after generating.</option> 401 <option value="gentest" selected="true">Test with planemo after generating.</option>
349 <option value="gentestinstall" selected="true">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> 402 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
350 </param> 403 </param>
351 <when value="generate"> 404 <when value="generate">
352 <param name="galaxy_apikey" value="" type="hidden" ></param> 405 <param name="galaxy_apikey" value="" type="hidden" ></param>
353 <param name="toolshed_apikey" value="" type="hidden" ></param> 406 <param name="toolshed_apikey" value="" type="hidden" ></param>
354 <param name="galaxy_url" value="" type="hidden" ></param> 407 <param name="galaxy_url" value="" type="hidden" ></param>
414 <param name="input_formats" value="txt" /> 467 <param name="input_formats" value="txt" />
415 <param name="input_label" value="input" /> 468 <param name="input_label" value="input" />
416 <param name="input_help" value="help" /> 469 <param name="input_help" value="help" />
417 <param name="tool_name" value="pyrevpos" /> 470 <param name="tool_name" value="pyrevpos" />
418 <param name="parampass" value="positional" /> 471 <param name="parampass" value="positional" />
419 <param name="make_Tool" value="generate" /> 472 <param name="make_Tool" value="gentest" />
420 <param name="tool_version" value="0.01" /> 473 <param name="tool_version" value="0.01" />
421 <param name="tool_desc" value="positional reverse" /> 474 <param name="tool_desc" value="positional reverse" />
422 <param name="help_text" value="help text goes here" /> 475 <param name="help_text" value="help text goes here" />
423 <param name="packages" value="python"/> 476 <param name="packages" value="python"/>
424 <param name="history_name" value="output2" /> 477 <param name="history_name" value="output2" />
513 rs.reverse() 566 rs.reverse()
514 o.write(''.join(rs)) 567 o.write(''.join(rs))
515 o.write('\n') 568 o.write('\n')
516 o.close() 569 o.close()
517 570
571 R script to draw some plots - use a collection.
572
573 ::
574
575
576 \# note this script takes NO input because it generates random data
577 dir.create('plots')
578 for (i in 1:10) {
579 foo = runif(100)
580 bar = rnorm(100)
581 bar = foo + 0.05*bar
582 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
583 plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
584 dev.off()
585 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
586 bar = as.matrix(foo)
587 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
588 heatmap(bar,main='Random Heatmap')
589 dev.off()
590 }
591
518 592
519 593
520 Paper_ 594 Paper_
521 595
522 *Licensing* 596 *Licensing*