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comparison DockerToolFactory.xml @ 0:0fa46413d0d9 draft

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planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
author mvdbeek
date Sat, 03 Oct 2015 08:34:39 -0400
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-1:000000000000 0:0fa46413d0d9
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="rgTF" name="docker_tool_factory" version="0.1.3">
3 <description>Makes scripts into tools using Docker</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="9.10">ghostscript</requirement>
9 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
10 <requirement type="package" version="0.4.0">docker-py</requirement>
11 </requirements>
12 <command interpreter="python"><![CDATA[
13 DockerToolFactory.py --script_path "$runme" --interpreter "$interpreter"
14 --tool_name "$tool_name" --user_email "$__user_email__"
15 #if $generate_simple_output.make_TAB=="yes":
16 --output_tab "$tab_file"
17 #end if
18 #if $makeMode.make_Tool=="yes":
19 #if generate_simple_output.make_TAB=="yes":
20 --output_format "$out_format"
21 #end if
22 --make_Tool "$makeMode.make_Tool"
23 --tool_desc "$makeMode.tool_desc"
24 --tool_version "$makeMode.tool_version"
25 --new_tool "$new_tool"
26 --help_text "$helpme"
27 #if $make_HTML.value=="yes":
28 --include_dependencies "${makeMode.include_deps}"
29 #end if
30 #end if
31 #if $make_HTML.value=="yes":
32 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
33 #else:
34 --output_dir "."
35 #end if
36 #if $additional_parameters != 'None':
37 #for i in $additional_parameters:
38 --additional_parameters
39 "$i.param_name, $i.param_value"
40 #end for
41 #end if
42 #if $input_files != 'None':
43 --input_tab
44 #for i in $input_files:
45 $i.input
46 #end for
47 #for i in $input_files:
48 --input_format
49 #if str($i.in_format) == "None":
50 "Any"
51 #else
52 "$i.in_format"
53 #end if
54 #end for
55 #end if
56 ]]>
57 </command>
58 <configfiles>
59 <configfile name="runme">$dynScript</configfile>
60 <configfile name="helpme">
61 #if $makeMode.make_Tool == "yes":
62 ${makeMode.help_text}
63 #end if
64 </configfile>
65 </configfiles>
66 <inputs>
67 <repeat name="input_files" title="Select input files">
68 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
69 <param name="in_format" type="select" optional="true" multiple="true"
70 label="Optional: Select the allowed input datatype(s) for your tool/script">
71 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
72 <column name="value" index="0"/>
73 </options>
74 </param>
75 </repeat>
76 <repeat name="additional_parameters" title="Set additional parameters">
77 <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
78 <sanitizer invalid_char="">
79 <valid initial="string.letters,string.digits">
80 <add value="@_."/>
81 </valid>
82 >
83 </sanitizer>
84 </param>
85 <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
86 <sanitizer>
87 <valid initial="string.printable">
88 </valid>
89 <mapping initial="none"/>
90 </sanitizer>
91 </param>
92 </repeat>
93 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs"
94 size="60"
95 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
96 <sanitizer invalid_char="">
97 <valid initial="string.printable"/>
98 </sanitizer>
99 </param>
100 <conditional name="makeMode">
101 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry"
102 help="Ready to deploy securely!" size="60">
103 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
104 <option value="" selected="true">No. Just run the script please</option>
105 </param>
106 <when value="yes">
107 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses"
108 type="text" value="0.01"
109 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
110 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
111 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)"/>
112 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
113 size="8x120" value="**What it Does**"
114 help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html">
115 <sanitizer>
116 <valid initial="string.printable">
117 </valid>
118 <mapping initial="none"/>
119 </sanitizer>
120 </param>
121 <param name="include_deps" type="select"
122 label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
123 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
124 <option value="">Rely on system ghostscript and graphicsmagick rather than include these as
125 dependencies
126 </option>
127 <option value="yes" selected="true">Include dependencies so target installations will always work if
128 HTML is being generated
129 </option>
130 </param>
131
132 </when>
133 <when value="">
134 </when>
135 </conditional>
136 <param name="out_format" type="text" value="txt" hidden="True"/>
137 <param name="make_HTML" type="select"
138 label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
139 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
140 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
141 <option value="" selected="true">No, no HTML output file thanks</option>
142 </param>
143 <conditional name="generate_simple_output">
144 <param name="make_TAB" type="select"
145 label="Create a new history output alongside the HTML file specified above"
146 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
147 <option value="yes" selected="true">My script writes to a new history output</option>
148 <option value="no">I do not want a new history output file</option>
149 </param>
150 <when value="yes">
151 <param name="out_format" type="select" label="Select the datatype that your tool/script produces"
152 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" optional="True">
153 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
154 <column name="value" index="0"/>
155 </options>
156 </param>
157 </when>
158 <when value="no">
159 <param name="out_format" type="text" value="txt" optional="True" hidden="True"/>
160 </when>
161 </conditional>
162 <param name="interpreter" type="select" label="Select the interpreter for your code">
163 <option value="Rscript" selected="true">Rscript</option>
164 <option value="python">python</option>
165 <option value="perl">perl</option>
166 <option value="sh">sh</option>
167 </param>
168 <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True"
169 size="8x120"
170 help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
171 <sanitizer>
172 <valid initial="string.printable">
173 </valid>
174 <mapping initial="none"/>
175 </sanitizer>
176 </param>
177 </inputs>
178 <outputs>
179 <!-- <data format_source="input" name="tab_file" label="${tool_name}.${out_format}"> -->
180 <data format_source="input" name="tab_file">
181 <filter>generate_simple_output['make_TAB'] == "yes"</filter>
182 <actions>
183 <action type="format">
184 <option type="from_param" name="out_format"/>
185 </action>
186 </actions>
187 </data>
188 <data format="html" name="html_file" label="${tool_name}.html">
189 <filter>make_HTML == "yes"</filter>
190 </data>
191 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
192 <filter>makeMode['make_Tool'] == "yes"</filter>
193 </data>
194 </outputs>
195 <tests>
196 <test>
197 <param name="interpreter" value="Rscript"/>
198 <param name="make_HTML" value="yes"/>
199 <param name="generate_simple_output|makeTAB" value="no"/>
200 <param name="out_format" value="txt"/>
201 <param name="dynScript" value="for (i in 1:10) {; foo = runif(100); bar = rnorm(100); bar = foo + bar; pdf(&quot;anotherplot.pdf&quot;); plot(1,2); dev.off();}"/>
202 <output name="html_file" file="html_output/My_dynamic_script_html.html" compare="diff"/>
203 </test>
204 </tests>
205 <expand macro="help_macro"/>
206 </tool>