annotate toolfactory/rgToolFactory2.xml @ 93:df1205dcf676 draft

Uploaded
author fubar
date Fri, 20 Nov 2020 00:34:13 +0000
parents 4663732f341e
children e8f35fec0f2f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
1 <tool id="rgtf2" name="toolfactory" version="2.00" profile="16.04" >
62
881bd8c81ac9 Uploaded
fubar
parents: 61
diff changeset
2 <description>Scripts into tools v2.0</description>
48
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=""
64
30847b2e105d Uploaded
fubar
parents: 63
diff changeset
26 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." />
49
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>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
59 <param name="input_help" type="text" value="" label="This will become help text on the form."
48
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">
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
88 <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
89 <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
48
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">
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
94 <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
48
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>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
112 <param name="param_label" type="text" value="" label="Enter this parameter's label for the form"
48
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>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
119 <param name="param_help" type="text" value="" label="Help for this parameter"
48
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>
56
68fbdbe35f08 Uploaded
fubar
parents: 55
diff changeset
133
93
df1205dcf676 Uploaded
fubar
parents: 90
diff changeset
134 <requirements>
90
4663732f341e Uploaded
fubar
parents: 89
diff changeset
135 <requirement type="package" version="0.72.0">planemo</requirement>
93
df1205dcf676 Uploaded
fubar
parents: 90
diff changeset
136 <!--<requirement type="package" version="0.4.11">galaxyxml</requirement>
90
4663732f341e Uploaded
fubar
parents: 89
diff changeset
137 <requirement type="package" version="0.14.0">bioblend</requirement>
93
df1205dcf676 Uploaded
fubar
parents: 90
diff changeset
138 <requirement type="package" version="0.10.6">ephemeris</requirement> -->
79
2d0272e730d1 Uploaded
fubar
parents: 77
diff changeset
139 </requirements>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
140
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
141 <command ><![CDATA[
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
142 #import os
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
143 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
144 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
76
46db8143adb7 Uploaded
fubar
parents: 73
diff changeset
145 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
146 #else:
76
46db8143adb7 Uploaded
fubar
parents: 73
diff changeset
147 python3 $__tool_directory__/rgToolFactory2.py
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
148 #if len(str($cl_prefix)) > 3:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
149 --cl_prefix "$cl_prefix"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
150 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
151 #if $cover.commover == "yes":
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
152 #if len(str($cover.command_override)) > 10:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
153 --command_override "$commandoverride"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
154 #end if
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
155 #if len(str($cover.test_override)) > 10:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
156 --test_override "$testoverride"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
157 #end if
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
158 #end if
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
159 --packages "$packages"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
160 #if $usescript.choosescript == "yes":
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
161 --script_path "$runme"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
162 --sysexe "$usescript.scriptrunner"
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
163 #end if
85
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
164 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" --parampass "$ppass.parampass"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
165
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
166 #if str($makeMode.make_Tool)!="runonly":
85
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
167 --make_Tool "$makeMode.make_Tool"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
168 --tool_desc "$makeMode.tool_desc"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
169 --tool_version "$makeMode.tool_version"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
170 --help_text "$helpme"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
171 --new_tool "$new_tool"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
172 --toolshed_api_key "$makeMode.toolshed_apikey"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
173 --galaxy_api_key "$makeMode.galaxy_apikey"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
174 --toolshed_url "$makeMode.toolshed_url"
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
175 --galaxy_url "$makeMode.galaxy_url"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
176 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
177 #if $ppass.parampass != '0':
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
178 #if str($ppass.edit_params) == "yes":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
179 --edit_additional_parameters
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
180 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
181 #for apar in $ppass.additional_parameters:
85
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
182 --additional_parameters "$apar.param_name~~~$apar.param_value~~~$apar.param_label~~~$apar.param_help~~~$apar.param_type~~~$apar.param_CL~~~$apar.param_CLprefixed"
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 #for $intab in $ppass.history_inputs:
85
933e68f8bdd2 Uploaded
fubar
parents: 82
diff changeset
186 --input_files "$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
187 #end for
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
188 #for $otab in $ppass.history_outputs:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
189 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
190 #end for
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
191 --galaxy_root "$__root_dir__"
73
95adf7148d9a Uploaded
fubar
parents: 72
diff changeset
192 --tool_dir "$__tool_directory__"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
193 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
194 ]]></command>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
195 <configfiles>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
196 <configfile name="runme">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
197 $usescript.dynScript
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
198 </configfile>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
199 <configfile name="commandoverride">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
200 #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
201 $cover.command_override
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
202 #end if
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
203 </configfile>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
204 <configfile name="testoverride">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
205 #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
206 $cover.test_override
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
207 #end if
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
208 </configfile>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
209 <configfile name="helpme">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
210 #if $makeMode.make_Tool != "runonly":
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
211 ${makeMode.help_text}
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
212 #else
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
213 $tool_name help goes here
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
214 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
215 </configfile>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
216 <configfile name="citeme">
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
217 #if $makeMode.make_Tool != "runonly":
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
218 #for $citation in $makeMode.citations:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
219 #if $citation.citation_type.type == "bibtex":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
220 **ENTRY**bibtex
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
221 ${citation.citation_type.bibtex}
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
222 #else
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
223 **ENTRY**doi
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
224 ${citation.citation_type.doi}
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
225 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
226 #end for
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
227 #end if
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
228 </configfile>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
229 </configfiles>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
230 <inputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
231 <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
232 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
233 <sanitizer invalid_char="">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
234 <valid initial="string.letters,string.digits">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
235 <add value="_"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
236 </valid>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
237 </sanitizer>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
238 </param>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
239 <param name="packages" type="text" value="" label="Conda dependencies as package name[:version, name:version...]. These will always be available when this tool executes"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
240 optional="false" help="Use :[ver] for specific version - 'bwa:0.17.0'. Default is latest. Will be used every time the tool is (re)run. Only Conda is currently supported" />
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
241
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
242 <conditional name="usescript">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
243 <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
244 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">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
245 <option value="no" selected="true">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
246 <option value="yes">Yes, a script is ready to be pasted below</option>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
247 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
248 <when value="no">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
249 <param name="dynScript" type="hidden" value="" />
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
250 <param name="scriptrunner" type="hidden" value="" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
251 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
252 <when value="yes">
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
253 <param name="scriptrunner" type="text" value="" label="Interpreter for the script pasted below - eg bash or python. Can be one of the dependencies named above or a system executable"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
254 help="Scripts are interpreted by the executable named here. Use bash for bash scripts, or a conda dependency such as R or Python for those scripts">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
255 <sanitizer invalid_char="">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
256 <valid initial="string.letters,string.digits">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
257 <add value="_"/>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
258 </valid>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
259 </sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
260 </param>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
261 <param name="dynScript" type="text" area="True" value="" label="Script for executable below to interpret. It can be one of the Conda dependency names "
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
262 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
263 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
264 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
265 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
266 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
267 </sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
268 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
269 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
270 </conditional>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
271
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
272 <conditional name="ppass">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
273 <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
274 <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
275 <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
276 <option value="0">Tool reads selected input file from STDIN and writes STDOUT with no parameters</option>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
277 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
278 <when value="argparse">
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="positional">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
283 <expand macro="io" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
284 <expand macro="additparam" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
285 </when>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
286 <when value="0">
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
287 <expand macro="io"/>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
288 </when>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
289 </conditional>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
290 <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
291 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
292 <conditional name="cover">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
293 <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
294 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
295 <option value="no" selected="true">No. Use automatically generated command/test XML </option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
296 <option value="yes">Yes. XML needed to override autogenerated command and/or test segments will be pasted below</option>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
297 </param>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
298 <when value="no">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
299 <param name="command_override" type="hidden" value="" />
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
300 <param name="test_override" type="hidden" value="" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
301 </when>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
302 <when value="yes">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
303 <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
304 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
305 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
306 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
307 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
308 <mapping initial="none"/>
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 </param>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
311 <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
312 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
313 <sanitizer>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
314 <valid initial="string.printable">
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
315 </valid>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
316 <mapping initial="none"/>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
317 </sanitizer>
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
318 </param>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
319 </when>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
320 </conditional>
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
321
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
322 <conditional name="makeMode">
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
323 <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"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
324 help="Installation in this Galaxy is optional" >
66
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
325 <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
326 <option value="gentest" selected="true">Test with planemo after generating.</option>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
327 <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
328 </param>
66
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
329 <when value="generate">
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
330 <param name="galaxy_apikey" value="" type="hidden" ></param>
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
331 <param name="toolshed_apikey" value="" type="hidden" ></param>
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
332 <param name="galaxy_url" value="" type="hidden" ></param>
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
333 <param name="toolshed_url" value="" type="hidden" ></param>
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
334 <expand macro="tool_metadata" />
bc1977b1f7b5 Uploaded
fubar
parents: 64
diff changeset
335 </when>
62
881bd8c81ac9 Uploaded
fubar
parents: 61
diff changeset
336 <when value="gentest">
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
337 <param name="galaxy_apikey" value="" type="hidden" ></param>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
338 <param name="toolshed_apikey" value="" type="hidden" ></param>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
339 <param name="galaxy_url" value="" type="hidden" ></param>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
340 <param name="toolshed_url" value="" type="hidden" ></param>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
341 <expand macro="tool_metadata" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
342 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
343 <when value="gentestinstall">
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
344 <param name="galaxy_url" type="text" value="http://localhost:8080" label="URL for the Galaxy server where the new tool should be installed"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
345 help="Default is localhost">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
346 <sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
347 <valid initial="string.printable">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
348 </valid>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
349 <mapping initial="none"/>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
350 </sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
351 </param>
64
30847b2e105d Uploaded
fubar
parents: 63
diff changeset
352 <param name="galaxy_apikey" type="text" value="fakekey" label="API key for the Galaxy to install the new tool"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
353 help="Cut and paste from the admin user properties screen">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
354 <sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
355 <valid initial="string.letters,string.digits">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
356 </valid>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
357 <mapping initial="none"/>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
358 </sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
359 </param>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
360 <param name="toolshed_url" type="text" value="http://localhost:9009" label="URL for the Toolshed where the new tool should be installed"
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
361 help="Default value is localhost:9009">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
362 <sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
363 <valid initial="string.printable">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
364 </valid>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
365 <mapping initial="none"/>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
366 </sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
367 </param>
64
30847b2e105d Uploaded
fubar
parents: 63
diff changeset
368 <param name="toolshed_apikey" type="text" value="fakekey" label="API key for the local toolshed to use when installing the tool"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
369 help="Cut and paste from the admin user properties screen">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
370 <sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
371 <valid initial="string.letters,string.digits">
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
372 </valid>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
373 <mapping initial="none"/>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
374 </sanitizer>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
375 </param>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
376
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
377 <expand macro="tool_metadata" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
378 </when>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
379 </conditional>
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
380
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
381 </inputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
382 <outputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
383
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
384 <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
385 <filter>makeMode['make_Tool'] != "runonly"</filter>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
386 </data>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
387
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
388 <collection name="TF_run_report" type="list" label="${tool_name} outputs">
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
389 <discover_datasets pattern="__name_and_ext__" directory="TF_run_report_tempdir" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
390 </collection>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391 </outputs>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392 <tests>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
393 <test>
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
394 <param name="user_email" value="admin@galaxy.org"/>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 <param name="input_files" value="input1_sample" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396 <param name="input_CL" value="1" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397 <param name="input_formats" value="txt" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 <param name="input_label" value="input" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 <param name="input_help" value="help" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 <param name="tool_name" value="pyrevpos" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 <param name="parampass" value="positional" />
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
402 <param name="make_Tool" value="generate" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 <param name="tool_version" value="0.01" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 <param name="tool_desc" value="positional reverse" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 <param name="help_text" value="help text goes here" />
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
406 <param name="packages" value="python"/>
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
407 <param name="history_name" value="output2" />
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408 <param name="history_format" value="txt" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
409 <param name="history_CL" value="2" />
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
410 <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
411 <param name="choosescript" value="yes" />
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
412 <param name="script_path" value="$runme"/>
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
413 <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
414
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
415 </test>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
416 </tests>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
417 <help>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
418
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
419 .. class:: warningmark
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
420
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
421 **Details and attribution**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
422 (see GTF_)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
423
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
424 **Local Admins ONLY**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
425 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
426
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
427 **If you find a bug**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
428 Please raise an issue, or even better, submit a pull request fixing it, on the github repository GTF_
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
429
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
430 **What it does**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
431 This tool optionally generates normal workflow compatible first class Galaxy tools
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
432
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 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
434 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
435 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
436
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 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
438 These can be editable by the downstream user or baked in.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 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
441 set of outputs - these are used to construct a test for the new tool.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 If tool generation is required, a new tarball compatible with any Galaxy toolshed is created.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 installed into any toolshed from where it can be installed into your Galaxy.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 .. class:: warningmark
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 **Note to system administrators**
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 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
452 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
453
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 .. class:: warningmark
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 **Use on public servers** is STRONGLY discouraged for obvious reasons
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 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
459 We recommend that you follow the good code hygiene practices associated with safe toolshed practices.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 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
462
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 ::
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 # reverse order of text by row
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 import sys
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 inp = sys.argv[1]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 outp = sys.argv[2]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 i = open(inp,'r').readlines()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 o = open(outp,'w')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 for row in i:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 rs = row.rstrip()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 rs = list(rs)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 rs.reverse()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 o.write(''.join(rs))
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 o.write('\n')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 o.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 With argparse style parameters:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 ::
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 # reverse order of text by row
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484 import argparse
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 parser = argparse.ArgumentParser()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
486 a = parser.add_argument
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 a('--infile',default='')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
488 a('--outfile',default=None)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
489 args = parser.parse_args()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
490 inp = args.infile
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
491 outp = args.outfile
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
492 i = open(inp,'r').readlines()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
493 o = open(outp,'w')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
494 for row in i:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
495 rs = row.rstrip()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
496 rs = list(rs)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
497 rs.reverse()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
498 o.write(''.join(rs))
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
499 o.write('\n')
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
500 o.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
501
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
502
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
503
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
504 Paper_
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
505
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
506 *Licensing*
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
507
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
508 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
509 All rights reserved.
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
510 Licensed under the LGPL_
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
511
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
512 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
513 .. _GTF: https://github.com/fubar2/toolfactory
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
514 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
515
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
516
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
517 </help>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
518 <citations>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
519 <citation type="doi">10.1093/bioinformatics/bts573</citation>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
520 </citations>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
521 </tool>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
522
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
523