annotate toolfactory/rgToolFactory2.xml @ 3:290f552d7e05 draft default tip

Uploaded
author fubar
date Sat, 17 Apr 2021 22:58:34 +0000
parents 48458b0369aa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
1 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
2 <description>Scripts into tools v2.0</description>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
3 <macros>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
4 <xml name="singleText">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
5 <param name="param_value" type="text" value="" label="Enter this parameter's default text value">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
6 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
7 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
8 <xml name="singleInt">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
9 <param name="param_value" type="integer" value="" label="Enter this parameter's default integer value" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
10 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
11 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
12 <xml name="singleFloat">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
13 <param name="param_value" type="float" value="" label="Enter this parameter's default value">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
14 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
15 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
16 <xml name="singleBoolean">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
17 <param name="param_value" type="boolean" value="" label="Enter this parameter's default value" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
18 <param name="truevalue" type="text" value="True" label="Command line value to emit when True" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
19 <param name="falsevalue" type="boolean" value="True" label="Command line value to emit when False" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
20 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
21 <xml name="selectText">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
22 <repeat name="selectTexts" title="Add each option to be presented in a text select box" min="2" default="2"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
23 help="Each text added here will also have a value to be emitted on the command line when the text is chosen">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
24 <param name="select_text" type="text" value="" label="Enter the explanatory text the user will see for this choice" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
25 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
26 <param name="select_value" type="text" value="" label="Enter the value for the command line when the user selects this option">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
27 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
28 </repeat>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
29 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
30 <xml name="tool_metadata">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
31 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
33 <param name="tool_desc" label="Tool Synopsis" type="text" value=""
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
34 help="Supply a brief tool description for the Galaxy tool menu entry" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
35 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
36 value="**What it Does**"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
37 help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
38 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
39 <valid initial="string.printable" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
40 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
41 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
42 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
43 <repeat name="citations" title="Citation">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
44 <conditional name="citation_type">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
45 <param name="type" type="select" display="radio" label="Citation Type">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
46 <option value="doi">DOI</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
47 <option value="bibtex">BibTeX</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
48 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
49 <when value="doi">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
50 <param name="doi" label="DOI" type="text" value=""
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
51 help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) to be cited when this tool is used in published research." />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
52 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
53 <when value="bibtex">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
54 <param name="bibtex" label="BibTex" type="text" area="true"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
55 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
56 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
57 <valid initial="string.printable" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
58 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
59 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
60 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
61 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
62 </conditional>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
63 </repeat>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
64 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
65 <xml name="io">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
66 <section name="io" title="Input and output files" expanded="true">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
67 <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable."
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
69 <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
70 help=""/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
71 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
72 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
73 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
74 <column name="value" index="0"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
75 </options>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
76 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
77 <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
78 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
79 <param name="input_help" type="text" value="" label="This will become help text on the form." >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
80 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
81 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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="">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
83 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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."/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
85 </repeat>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
87 help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
88 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
89 help="No spaces! Argparse will also use this name as --[name]">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
90 <sanitizer invalid_char="_">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
91 <valid initial="string.ascii_letters,string.digits" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
92 <add value="_" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
93 </valid>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
94 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
95 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
96 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
97 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
98 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
99 <column name="value" index="0"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
100 </options>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
101 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
102 <param name="history_CL" type="text" label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
103 help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
104 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
105 help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
106 </repeat>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
107 <repeat name="collection_outputs" title="zero or more new history collections to appear in the user history after the tool runs"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
108 help="Hides outputs not needed for downstream tools such as images and intermediate reports." default="0">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
109 <param name="name" type="text" label="Name for new collection with all outputs not individually passed to history outputs"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
111 <sanitizer invalid_char="_">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
112 <valid initial="string.ascii_letters,string.digits" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
113 <add value="_" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
114 </valid>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
115 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
116 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
117 <param name="kind" type="select" multiple="false" label="Select the kind of collection for this output"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
118 help="">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
119 <option value="list" selected="true">List</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
120 <option value="paired">Paired</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
121 <option value="list:paired">List of paired</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
122 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
123 <param name="label" type="text" label="Label for this collection" help="" value=""/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
124 <param name="discover" type="text" label="Discover datasets expression" help="__name_and_ext__ should catch all filenames with extensions" value="__name_and_ext__"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
125 </repeat>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
126
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
127 </section>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
128 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
129 <xml name="additparam">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
130 <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
131 <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
133 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
134 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
135 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
136 <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
137 help="See examples below to see how these can be parsed by scripts in the various languages">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
138 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
139 <sanitizer invalid_char="">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
140 <valid initial="string.ascii_letters,string.digits"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
141 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
142 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
143 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
144 <conditional name="ap_type">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
145 <param name="param_type" type="select" label="Select the type for this parameter">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
146 <option value="text" selected="true">Text string</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
147 <option value="integer">Integer</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
148 <option value="float">Float</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
149 <option value="boolean">Boolean</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
150 <option value="selecttext">Select text string</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
151 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
152 <when value = "text">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
153 <expand macro="singleText" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
154 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
155 <when value = "integer">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
156 <expand macro="singleInt" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
157 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
158 <when value = "float">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
159 <expand macro="singleFloat" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
160 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
161 <when value = "boolean">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
162 <expand macro="singleBoolean" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
163 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
164 <when value = "selecttext">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
165 <expand macro="selectText" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
166 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
167 </conditional>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
168 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
169 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
170 <param name="param_help" type="text" value="" label="Help for this parameter">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
171 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
172 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
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="" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
174 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
175 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
176 <param name="param_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this as many times as needed." />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
177 </repeat>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
178 </section>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
179 </xml>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
180 </macros>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
181
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
182 <requirements>
1
48458b0369aa Uploaded
fubar
parents: 0
diff changeset
183 <requirement type="package" version="0.4.14">galaxyxml</requirement>
0
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
184 <requirement type="package" version="0.74.3">planemo</requirement>
1
48458b0369aa Uploaded
fubar
parents: 0
diff changeset
185 <container type="docker">quay.io/biocontainers/mulled-v2-0a86ccf22d71945a175383bcea5edd6b51c25ed0:55f1b8132a10ad91f0016ba9f4c692627ca2d25b-0</container>
0
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
186 </requirements>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
187
1
48458b0369aa Uploaded
fubar
parents: 0
diff changeset
188 <command detect_errors="exit_code"><![CDATA[
0
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
189 #import os
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
190 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
191 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
192 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
193 #else:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
194 python3 $__tool_directory__/rgToolFactory2.py
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
195 #if len(str($cl_suffix)) > 0:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
196 --cl_suffix "$cl_suffix"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
197 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
198 #if $cover.commover == "yes":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
199 #if len(str($cover.command_override)) > 10:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
200 --command_override "$commandoverride"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
201 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
202 #if len(str($cover.test_override)) > 10:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
203 --test_override "$testoverride"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
204 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
205 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
206 --packages "$deps.packages"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
207 #if $deps.usescript.choosescript == "yes":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
208 --script_path "$runme"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
209 --sysexe "$deps.usescript.scriptrunner"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
210 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
211 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$io_param.ppass.parampass"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
212
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
213 #if str($make.makeMode.make_Tool)!="runonly":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
214 --make_Tool "$make.makeMode.make_Tool"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
215 --tool_desc "$make.makeMode.tool_desc"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
216 --tool_version "$make.makeMode.tool_version"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
217 --help_text "$helpme"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
218 --new_tool "$new_tool"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
219 --toolshed_api_key "$make.makeMode.toolshed_apikey"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
220 --galaxy_api_key "$make.makeMode.galaxy_apikey"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
221 --toolshed_url "$make.makeMode.toolshed_url"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
222 --galaxy_url "$make.makeMode.galaxy_url"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
223 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
224 #if $io_param.ppass.parampass != '0':
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
225 #if str($io_param.ppass.addparam.edit_params) == "yes":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
226 --edit_additional_parameters
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
227 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
228 #for $apar in $io_param.ppass.addparam.additional_parameters:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
229 #if $apar.ap_type.param_type=="selecttext":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
230 --selecttext_parameters '{"name":"$apar.param_name", "label":"$apar.param_label", "help":"$apar.param_help",
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
231 "type":"$apar.ap_type.param_type","CL":"$apar.param_CL","override":"$apar.param_CLprefixed","value": [
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
232 #for $i,$st in enumerate($apar.ap_type.selectTexts):
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
233 "$st.select_value"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
234 #if ($i < (len($apar.ap_type.selectTexts)-1)):
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
235 ,
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
236 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
237 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
238 ], "texts": [
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
239 #for $i,$st in enumerate($apar.ap_type.selectTexts):
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
240 "$st.select_text"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
241 #if ($i < (len($apar.ap_type.selectTexts)-1)):
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
242 ,
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
243 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
244
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
245 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
246 ]
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
247 }'
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
248 #else:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
249 --additional_parameters '{"name": "$apar.param_name", "value": "$apar.ap_type.param_value", "label": "$apar.param_label", "help": "$apar.param_help",
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
250 "type": "$apar.ap_type.param_type","CL": "$apar.param_CL","override": "$apar.param_CLprefixed", "repeat": "$apar.param_repeat"}'
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
251 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
252 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
253 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
254 #for $intab in $io_param.ppass.io.history_inputs:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
255 --input_files '{"name": "$intab.input_files", "CL": "$intab.input_CL", "format": "$intab.input_formats", "label": "$intab.input_label", "help": "$intab.input_help", "repeat": "$intab.input_repeat"}'
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
256 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
257 #for $otab in $io_param.ppass.io.history_outputs:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
258 --output_files '{"name": "$otab.history_name", "format": "$otab.history_format", "CL": "$otab.history_CL", "test": "$otab.history_test"}'
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
259 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
260 #for $collect in $io_param.ppass.io.collection_outputs:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
261 --collection '{"name": "$collect.name", "kind": "$collect.kind", "discover": "$collect.discover", "label": "$collect.label"}'
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
262 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
263 --galaxy_root "$__root_dir__"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
264 --tool_dir "$__tool_directory__"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
265 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
266 ]]></command>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
267 <configfiles>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
268 <configfile name="runme">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
269 $deps.usescript.dynScript
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
270 </configfile>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
271 <configfile name="commandoverride">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
272 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
273 $cover.command_override
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
274 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
275 </configfile>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
276 <configfile name="testoverride">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
277 #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
278 $cover.test_override
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
279 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
280 </configfile>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
281 <configfile name="helpme">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
282 #if $make.makeMode.make_Tool != "runonly":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
283 ${make.makeMode.help_text}
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
284 #else
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
285 $tool_name help goes here
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
286 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
287 </configfile>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
288 <configfile name="citeme">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
289 #if $make.makeMode.make_Tool != "runonly":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
290 #for $citation in $make.makeMode.citations:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
291 #if $citation.citation_type.type == "bibtex":
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
292 **ENTRY**bibtex
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
293 ${citation.citation_type.bibtex}
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
294 #else
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
295 **ENTRY**doi
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
296 ${citation.citation_type.doi}
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
297 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
298 #end for
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
299 #end if
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
300 </configfile>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
301 </configfiles>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
302 <inputs>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
303 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
304 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
305 <sanitizer invalid_char="">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
306 <valid initial="string.ascii_lowercase,string.digits">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
307 <add value="_"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
308 </valid>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
309 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
310 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
311
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
312 <section name="deps" title="Dependencies, optional script and script interpreter" expanded="true">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
313
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
314 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
315 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" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
316
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
317 <conditional name="usescript">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
318 <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"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
319 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">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
320 <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
321 <option value="yes" selected="true">Yes, a script is ready to be pasted below</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
322 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
323 <when value="no">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
324 <param name="dynScript" type="hidden" value="" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
325 <param name="scriptrunner" type="hidden" value="" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
326 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
327 <when value="yes">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
328 <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"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
329 help="Scripts are interpreted by the executable named here. For conda r-base, 'Rscript --vanilla' or for conda planemo, 'planemo test' for example">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
330 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
331 <param name="dynScript" type="text" area="True" value="" label="Script for executable above to interpret. It can be one of the Conda dependency names "
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
332 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
333 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
334 <valid initial="string.printable"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
335 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
336 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
337 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
338 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
339 </conditional>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
340 </section>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
341 <section name="io_param" title="Data file input, output and settings forming the executable or script command line" expanded="true">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
342 <conditional name="ppass">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
343 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
344 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
345 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
346 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
347 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
348 <when value="argparse">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
349 <expand macro="io" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
350 <expand macro="additparam" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
351 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
352 <when value="positional">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
353 <expand macro="io" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
354 <expand macro="additparam" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
355 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
356 <when value="0">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
357 <expand macro="io"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
358 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
359 </conditional>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
360 </section>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
361 <param name="cl_suffix" type="text" value="" label="Suffix for generated command line. Useful for bash post processing. Use override below to replace completely"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
362 help="';' separated bash commands can be used here for post processing - added at end of autogenerated command line">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
363 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
364 <valid initial="string.printable" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
365 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
366 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
367 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
368 <conditional name="cover">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
369 <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
370 help = "For arbitrary and artfull command lines. All i/o and parameters must be passed. Choose No unless needed. Not for the faint of heart">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
371 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
372 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
373 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
374 <when value="no">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
375 <param name="command_override" type="hidden" value="" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
376 <param name="test_override" type="hidden" value="" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
377 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
378 <when value="yes">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
379 <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
380 help="For arbitrary and artfull command lines. All i/o and parameters must be passed. Leave blank unless needed. Not for the faint of heart">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
381 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
382 <valid initial="string.printable"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
383 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
384 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
385 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
386 <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
387 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
388 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
389 <valid initial="string.printable" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
390 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
391 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
392 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
393 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
394 </conditional>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
395 <section name="make" title="Generate, toolshed and local Galaxy installation options" expanded="true">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
396 <conditional name="makeMode">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
397 <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"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
398 help="Installation in this Galaxy is optional" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
399 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
400 <option value="gentest" selected="true">Test with planemo after generating.</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
401 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
402 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
403 <when value="generate">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
404 <param name="galaxy_apikey" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
405 <param name="toolshed_apikey" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
406 <param name="galaxy_url" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
407 <param name="toolshed_url" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
408 <expand macro="tool_metadata" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
409 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
410 <when value="gentest">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
411 <param name="galaxy_apikey" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
412 <param name="toolshed_apikey" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
413 <param name="galaxy_url" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
414 <param name="toolshed_url" value="" type="hidden" ></param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
415 <expand macro="tool_metadata" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
416 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
417 <when value="gentestinstall">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
418 <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
419 help="Default is localhost">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
420 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
421 <valid initial="string.printable" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
422 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
423 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
424 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
425 <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
426 help="Cut and paste from the admin user properties screen">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
427 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
428 <valid initial="string.ascii_letters,string.digits" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
429 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
430 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
431 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
432 <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
433 help="Default value is localhost:9009">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
434 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
435 <valid initial="string.printable" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
436 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
437 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
438 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
439 <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool"
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
440 help="Cut and paste from the admin user properties screen">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
441 <sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
442 <valid initial="string.ascii_letters,string.digits" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
443 <mapping initial="none"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
444 </sanitizer>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
445 </param>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
446 <expand macro="tool_metadata" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
447 </when>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
448 </conditional>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
449 </section>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
450 </inputs>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
451 <outputs>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
452
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
453 <data format="toolshed.gz" name="new_tool" label="${tool_name}_toolshed.gz" >
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
454 <filter>makeMode['make_Tool'] != "runonly"</filter>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
455 </data>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
456
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
457 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
458 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
459 </collection>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
460 </outputs>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
461 <tests>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
462 <test>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
463 <param name="user_email" value="admin@galaxy.org"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
464 <param name="input_files" value="input1_sample" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
465 <param name="input_CL" value="1" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
466 <param name="input_formats" value="txt" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
467 <param name="input_label" value="input" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
468 <param name="input_help" value="help" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
469 <param name="tool_name" value="pyrevpos" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
470 <param name="parampass" value="positional" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
471 <param name="make_Tool" value="gentest" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
472 <param name="tool_version" value="0.01" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
473 <param name="tool_desc" value="positional reverse" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
474 <param name="help_text" value="help text goes here" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
475 <param name="packages" value="python"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
476 <param name="history_name" value="output2" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
477 <param name="history_format" value="txt" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
478 <param name="history_CL" value="2" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
479 <param name="dynScript" value="import sys; inp = sys.argv[1]; outp = sys.argv[2]; inlist = open(inp,'r').readlines(); o = open(outp,'w'); rs = [''.join(list(reversed(x.rstrip()))) for x in inlist]; o.write('\n'.join(rs)); o.close()"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
480 <param name="choosescript" value="yes" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
481 <param name="script_path" value="$runme"/>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
482 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
483 </test>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
484 </tests>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
485 <help>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
486
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
487 .. class:: warningmark
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
488
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
489 **Details and attribution**
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
490 (see GTF_)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
491
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
492 **Local Admins ONLY**
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
493 Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
494
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
495 **If you find a bug**
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
496 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
497
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
498 **What it does**
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
499 This tool optionally generates normal workflow compatible first class Galaxy tools
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
500
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
501 Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
502 Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
503 Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
504
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
505 Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
506 These can be editable by the downstream user or baked in.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
507
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
508 When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
509 set of outputs - these are used to construct a test for the new tool.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
510
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
511 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
512 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
513 installed into any toolshed from where it can be installed into your Galaxy.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
514
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
515
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
516 .. class:: warningmark
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
517
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
518 **Note to system administrators**
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
519 This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
520 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
521
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
522 .. class:: warningmark
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
523
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
524 **Use on public servers** is STRONGLY discouraged for obvious reasons
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
525
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
526 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
527 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
528
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
529 Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
530
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
531 ::
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
532
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
533 # reverse order of text by row
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
534 import sys
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
535 inp = sys.argv[1]
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
536 outp = sys.argv[2]
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
537 i = open(inp,'r').readlines()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
538 o = open(outp,'w')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
539 for row in i:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
540 rs = row.rstrip()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
541 rs = list(rs)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
542 rs.reverse()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
543 o.write(''.join(rs))
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
544 o.write('\n')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
545 o.close()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
546
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
547 With argparse style parameters:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
548
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
549 ::
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
550
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
551 # reverse order of text by row
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
552 import argparse
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
553 parser = argparse.ArgumentParser()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
554 a = parser.add_argument
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
555 a('--infile',default='')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
556 a('--outfile',default=None)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
557 args = parser.parse_args()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
558 inp = args.infile
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
559 outp = args.outfile
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
560 i = open(inp,'r').readlines()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
561 o = open(outp,'w')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
562 for row in i:
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
563 rs = row.rstrip()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
564 rs = list(rs)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
565 rs.reverse()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
566 o.write(''.join(rs))
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
567 o.write('\n')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
568 o.close()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
569
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
570 R script to draw some plots - use a collection.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
571
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
572 ::
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
573
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
574
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
575 \# note this script takes NO input because it generates random data
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
576 dir.create('plots')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
577 for (i in 1:10) {
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
578 foo = runif(100)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
579 bar = rnorm(100)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
580 bar = foo + 0.05*bar
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
581 pdf(paste('plots/yet',i,"anotherplot.pdf",sep='_'))
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
582 plot(foo,bar,main=paste("Foo by Bar plot \#",i),col="maroon", pch=3,cex=0.6)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
583 dev.off()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
584 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
585 bar = as.matrix(foo)
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
586 pdf(paste('plots/yet',i,"anotherheatmap.pdf",sep='_'))
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
587 heatmap(bar,main='Random Heatmap')
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
588 dev.off()
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
589 }
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
590
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
591
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
592
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
593 Paper_
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
594
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
595 *Licensing*
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
596
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
597 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
598 All rights reserved.
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
599 Licensed under the LGPL_
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
600
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
601 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
602 .. _GTF: https://github.com/fubar2/toolfactory
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
603 .. _Paper: https://academic.oup.com/bioinformatics/article/28/23/3139/192853
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
604
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
605
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
606 </help>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
607 <citations>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
608 <citation type="doi">10.1093/bioinformatics/bts573</citation>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
609 </citations>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
610 </tool>
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
611
fc50a3f507ab Need a new repo - old tool_factory_2 is broken
fubar
parents:
diff changeset
612