annotate toolfactory/rgToolFactory2.xml @ 52:e8bf01166d74 draft

Uploaded
author fubar
date Sun, 30 Aug 2020 07:09:26 -0400
parents bf432f4486c7
children dcd66b623000
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
52
e8bf01166d74 Uploaded
fubar
parents: 50
diff changeset
1 <tool id="rgTF2" name="toolfactory" version="3.00" profile="16.04" >
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
2 <description>Scripts into tools</description>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
3 <macros>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
4 <xml name="tool_metadata">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
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"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
7 <param name="tool_desc" label="Tool Description" type="text" value=""
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
8 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
9 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
10 value="**What it Does**"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
11 help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
12 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
13 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
14 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
15 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
16 </sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
17 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
18 <repeat name="citations" title="Citation">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
19 <conditional name="citation_type">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
20 <param name="type" type="select" display="radio" label="Citation Type">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
21 <option value="doi">DOI</option>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
22 <option value="bibtex">BibTeX</option>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
23 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
24 <when value="doi">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
25 <param name="doi" label="DOI" type="text" value=""
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
26 help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
27 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
28 <when value="bibtex">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
29 <param name="bibtex" label="BibTex" type="text" area="true"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
30 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
31 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
32 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
33 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
34 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
35 </sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
36 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
37 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
38 </conditional>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
39 </repeat>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
40 </xml>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
41 <xml name="io">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
42 <repeat name="history_inputs" title="Add a data file from your history to pass in to the script. Use the '+' button as needed"
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
43 help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
44 <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" multiple="false"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
45 help=""/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
46 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
47 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
48 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
49 <column name="value" index="0"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
50 </options>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
51 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
52 <param name="input_label" type="text" value="" label="This will become the user prompt for the form so please make it informative"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
53 help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
54 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
55 <valid initial="string.printable"> <remove value='~~~'/> </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
56 <mapping initial="none"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
57 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
58 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
59 <param name="input_help" type="text" value="parameter_help" label="This will become help text on the form."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
60 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
61 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
62 <valid initial="string.printable"> <remove value='~~~'/> </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
63 <mapping initial="none"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
64 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
65 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
66 <param name="input_CL" type="text" label="Positional: ordinal integer. Argparse: argument name. STDIN if the executable/script expects it"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
67 help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
68 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
69 </repeat>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
70 <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
71 help="The name will become a history item for users of the new tool you are making containing one of it's outputs">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
72 <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help=""/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
73 <param name="history_format" type="select" multiple="false" label="Select the datatype for this output"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
74 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
75 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
76 <column name="value" index="0"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
77 </options>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
78 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
79 <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
80 help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
81 <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
82 help="Available options are diff:lines, sim_size" value="diff:2"/>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
83 </repeat>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
84 </xml>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
85 <xml name="additparam">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
86 <param name="edit_params" type="select" display="radio" label="Add any additional parameters to the generated tool form so they are user editable?"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
87 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
88 <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
89 <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
90 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
91
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
92 <repeat name="additional_parameters" title="Pass additional parameters to the script"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
93 help="See examples below to see how these can be parsed by scripts in the various languages">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
94 <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
95 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
96 <valid initial="string.letters,string.digits"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
97 <mapping initial="none"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
98 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
99 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
100 <param name="param_type" type="select" label="Select the type for this parameter">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
101 <option value="text" selected="true">text</option>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
102 <option value="integer">integer</option>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
103 <option value="float">float</option>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
104 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
105 <param name="param_value" type="text" value="" label="Enter this parameter's default value"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
106 help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" >
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
107 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
108 <valid initial="string.printable"> <remove value='~~~'/> </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
109 <mapping initial="none"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
110 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
111 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
112 <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
113 help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" >
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
114 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
115 <valid initial="string.printable"> <remove value='~~~'/> </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
116 <mapping initial="none"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
117 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
118 </param>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
119 <param name="param_help" type="text" value="parameter_help" label="Help for this parameter"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
120 help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" >
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
121 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
122 <valid initial="string.printable"> <remove value='~~~'/> </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
123 <mapping initial="none"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
124 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
125 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
126 <param name="param_CL" type="text" label="Positional ordinal | argparse argument name"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
127 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="" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
128 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
129 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
130 </repeat>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
131 </xml>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
132 </macros>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
133 <requirements>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
134 <requirement type="package" version="0.1">planemoenv</requirement>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
135 </requirements>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
136 <command ><![CDATA[
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
137 #import os
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
138 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
139 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
140 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
141 #else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
142 python3 $__tool_directory__/rgToolFactory2.py
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
143 #if len(str($cl_prefix)) > 3:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
144 --cl_prefix "$cl_prefix"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
145 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
146 #if $cover.commover == "yes":
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
147 #if len(str($cover.command_override)) > 10:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
148 --command_override "$commandoverride"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
149 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
150 #if len(str($cover.test_override)) > 10:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
151 --test_override "$testoverride"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
152 #end if
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
153 #end if
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
154 #if $interexe.dependency_model == "managed":
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
155 --packages "$interexe.packages"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
156 #else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
157 --sysexe "$interexe.sysexe"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
158 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
159 --tool_name="$tool_name" --user_email="$__user_email__" --citations="$citeme" --parampass="$ppass.parampass"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
160 #if $usescript.choosescript == "yes":
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
161 --script_path "$runme"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
162 #end if
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
163 #if str($makeMode.make_Tool)!="runonly":
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
164 --make_Tool="$makeMode.make_Tool"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
165 --tool_desc="$makeMode.tool_desc"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
166 --tool_version="$makeMode.tool_version"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
167 --help_text="$helpme"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
168 --new_tool="$new_tool"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
169 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
170 #if $ppass.parampass != '0':
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
171 #if str($ppass.edit_params) == "yes":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
172 --edit_additional_parameters
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
173 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
174 #for apar in $ppass.additional_parameters:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
175 --additional_parameters="$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
176 #end for
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
177 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
178 #for $intab in $ppass.history_inputs:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
179 --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
180 #end for
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
181 #for $otab in $ppass.history_outputs:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
182 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
183 #end for
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
184 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
185 ]]></command>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
186 <configfiles>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
187 <configfile name="runme">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
188 $usescript.dynScript
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
189 </configfile>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
190 <configfile name="commandoverride">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
191 #if $cover.commover == "yes" and len(str($cover.command_override).strip()) > 1:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
192 $cover.command_override
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
193 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
194 </configfile>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
195 <configfile name="testoverride">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
196 #if $cover.commover == "yes" and len(str($cover.test_override).strip()) > 1:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
197 $cover.test_override
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
198 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
199 </configfile>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
200 <configfile name="helpme">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
201 #if $makeMode.make_Tool != "runonly":
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
202 ${makeMode.help_text}
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
203 #else
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
204 $tool_name help goes here
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
205 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
206 </configfile>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
207 <configfile name="citeme">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
208 #if $makeMode.make_Tool != "runonly":
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
209 #for $citation in $makeMode.citations:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
210 #if $citation.citation_type.type == "bibtex":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
211 **ENTRY**bibtex
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
212 ${citation.citation_type.bibtex}
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
213 #else
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
214 **ENTRY**doi
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
215 ${citation.citation_type.doi}
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
216 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
217 #end for
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
218 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
219 </configfile>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
220 </configfiles>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
221 <inputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
222 <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs"
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
223 help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
224 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
225 <valid initial="string.letters,string.digits">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
226 <add value="_"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
227 </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
228 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
229 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
230
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
231 <conditional name="interexe">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
232 <param name="dependency_model" type="select" label="Dependency model: Conda managed external dependency or existing system executable"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
233 help = "If managed, the supplied package will become a requirement so must match the tool dependency resolver package name in conda.">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
234 <option value="managed" selected="true" >Use Conda managed dependencies for scripting (python, R,....) or command line packages (bwa,samtools)</option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
235 <option value="system" >Use a non-dependency managed system executable for scripting like bash or command line driven like sed or awk</option>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
236 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
237 <when value="managed">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
238 <param name="packages" type="text" value="" label="Package name[:version, name:version...] for Conda. First (e.g. python) will be called on generated command line"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
239 optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run." />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
240 <param name="sysexe" type="hidden" value="" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
241 </when>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
242 <when value="system">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
243 <param name="sysexe" type="text" value="" label="System executable to run. OS version - not Conda managed" optional="false"
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
244 help=".e.g bash, awk or other standard and relatively invariant unix utilities"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
245 <param name="packages" type="hidden" value="" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
246 </when>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
247 </conditional>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
248 <conditional name="usescript">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
249 <param name="choosescript" type="select" display="radio" label="Run a supplied script if the dependency reads one (e.g. python/R/bash)"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
250 help = "For script interpreters like Python or bash. Parameters and i/o below must match script's expectations">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
251 <option value="no" selected="true">No script required for the first dependency above - just parameters on the command line</option>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
252 <option value="yes">Yes, a script is ready to be pasted below for the chosen package</option>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
253 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
254 <when value="no">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
255 <param name="dynScript" type="hidden" value="" />
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
256 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
257 <when value="yes">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
258 <param name="dynScript" type="text" area="True" value="" label="Script for first dependency above (e.g. python) to interpret. "
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
259 help="Script must handle all i/o and parameters as specified below using the parameters and passing method chosen below">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
260 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
261 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
262 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
263 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
264 </sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
265 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
266 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
267 </conditional>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
268 <conditional name="ppass">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
269 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
270 <option value="argparse" selected="true">Argparse: passed in the form of --clname value</option>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
271 <option value="positional">Positional: Passed in the order of positional ordinals ...foo.bam bar.idx zot.xls</option>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
272 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
273 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
274 <when value="argparse">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
275 <expand macro="io" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
276 <expand macro="additparam" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
277 </when>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
278 <when value="positional">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
279 <expand macro="io" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
280 <expand macro="additparam" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
281 </when>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
282 <when value="0">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
283 <expand macro="io"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
284 </when>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
285 </conditional>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
286 <param name="cl_prefix" type="text" value="" label="Prefix for generated command line. Prepends generated i/o and parameter CL. Use override below to replace completely"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
287 help="Text will replace generated executable/script elements. Sometimes required before i/o and parameters in the generated command line." />
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
288 <conditional name="cover">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
289 <param name="commover" type="select" display="radio" label="Add Human wrought code to override the generated XML command and/or test section - DIY"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
290 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">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
291 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
292 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
293 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
294 <when value="no">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
295 <param name="command_override" type="hidden" value="" />
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
296 <param name="test_override" type="hidden" value="" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
297 </when>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
298 <when value="yes">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
299 <param name="command_override" type="text" area="True" value="" label="Optional. Human wrought command element override XML/template - e.g. for bwa"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
300 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">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
301 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
302 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
303 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
304 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
305 </sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
306 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
307 <param name="test_override" type="text" area="True" value="" label="Optional. Human wrought test element override XML/template - e.g. for bwa"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
308 help="For arbitrary and artfull scripts. Leave blank unless needed. Not for the faint of heart">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
309 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
310 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
311 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
312 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
313 </sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
314 </param>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
315 </when>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
316 </conditional>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
317
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
318 <conditional name="makeMode">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
319 <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"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
320 help="Testing and installation in this Galaxy are optional" >
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
321 <option value="runonly">Run this configuration in Galaxy (will run Planemo if command or test override in play)</option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
322 <option value="generate">Generate a toolshed ready archive.</option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
323 <option value="gentest" selected="true">Test with planemo after generating.</option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
324 <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
325 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
326 <when value="runonly"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
327 <when value="generate">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
328 <expand macro="tool_metadata" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
329 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
330 <when value="gentest">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
331 <expand macro="tool_metadata" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
332 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
333 <when value="gentestinstall">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
334 <expand macro="tool_metadata" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
335 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
336 </conditional>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
337
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
338 </inputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
339 <outputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
340
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
341 <data format="tgz" name="new_tool" label="${tool_name}_toolshed.tgz" >
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
342 <filter>makeMode['make_Tool'] != "runonly"</filter>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
343 </data>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
344
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
345 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
346 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
347 </collection>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
348 </outputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
349 <tests>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
350 <test>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
351 <param name="user_email" value="admin@galaxy.org"/>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
352 <param name="input_files" value="input1_sample" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
353 <param name="input_CL" value="1" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
354 <param name="input_formats" value="txt" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
355 <param name="input_label" value="input" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
356 <param name="input_help" value="help" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
357 <param name="tool_name" value="pyrevpos" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
358 <param name="parampass" value="positional" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
359 <param name="make_Tool" value="generate" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
360 <param name="tool_version" value="0.01" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
361 <param name="tool_desc" value="positional reverse" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
362 <param name="help_text" value="help text goes here" />
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
363 <param name="packages" value="python"/>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
364 <param name="history_name" value="output2" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
365 <param name="history_format" value="txt" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
366 <param name="history_CL" value="2" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
367 <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()"/>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
368 <param name="choosescript" value="yes" />
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
369 <param name="script_path" value="$runme"/>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
370 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
371 </test>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
372 </tests>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
373 <help>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
374
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
375 .. class:: warningmark
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
376
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
377 **Details and attribution**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
378 (see GTF_)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
379
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
380 **Local Admins ONLY**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
381 Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
382
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
383 **If you find a bug**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
384 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
385
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
386 **What it does**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
387 This tool optionally generates normal workflow compatible first class Galaxy tools
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
388
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
389 Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
390 Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391 Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
393 Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
394 These can be editable by the downstream user or baked in.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396 When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397 set of outputs - these are used to construct a test for the new tool.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 installed into any toolshed from where it can be installed into your Galaxy.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 .. class:: warningmark
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406 **Note to system administrators**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
409
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
410 .. class:: warningmark
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
411
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
412 **Use on public servers** is STRONGLY discouraged for obvious reasons
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
413
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
414 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.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
415 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
416
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
417 Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
418
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
419 ::
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
420
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
421 # reverse order of text by row
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
422 import sys
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
423 inp = sys.argv[1]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
424 outp = sys.argv[2]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
425 i = open(inp,'r').readlines()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
426 o = open(outp,'w')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
427 for row in i:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
428 rs = row.rstrip()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
429 rs = list(rs)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
430 rs.reverse()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
431 o.write(''.join(rs))
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
432 o.write('\n')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 o.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
434
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
435 With argparse style parameters:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
436
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 ::
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
438
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 # reverse order of text by row
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 import argparse
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 parser = argparse.ArgumentParser()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 a = parser.add_argument
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 a('--infile',default='')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 a('--outfile',default=None)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 args = parser.parse_args()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 inp = args.infile
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 outp = args.outfile
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 i = open(inp,'r').readlines()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 o = open(outp,'w')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 for row in i:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 rs = row.rstrip()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 rs = list(rs)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 rs.reverse()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 o.write(''.join(rs))
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 o.write('\n')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 o.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
460 Paper_
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
462 *Licensing*
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 All rights reserved.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 Licensed under the LGPL_
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 .. _GTF: https://github.com/fubar2/toolfactory
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 </help>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 <citations>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 <citation type="doi">10.1093/bioinformatics/bts573</citation>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 </citations>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 </tool>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479