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comparison rgToolFactory.xml @ 8:220885b2d7ee

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End to end test works. Add tests next
author ross lazarus ross.lazarus@gmail.com
date Sat, 02 Jun 2012 20:02:11 +1000
parents 7221619caefa
children e09c76551bed
comparison
equal deleted inserted replaced
7:7221619caefa 8:220885b2d7ee
3 <command interpreter="python"> 3 <command interpreter="python">
4 #if ( $__user_email__ not in ['ross.lazarus@gmail.com',] ): 4 #if ( $__user_email__ not in ['ross.lazarus@gmail.com',] ):
5 rgToolFactory.py --bad_user $__user_email__ 5 rgToolFactory.py --bad_user $__user_email__
6 #else: 6 #else:
7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
8 --tool_name "$tool_name" --input_tab "$input1" --user_email "${__user_email__}" 8 --tool_name "$tool_name" --input_tab "$input1"
9 #if $makeHTML.value=="yes" or $makeTool.value=="yes": 9 #if $make_HTML.value=="yes" or $factory.make_Tool=="yes":
10 --output_dir "$html_file.files_path" --output_html "$html_file" 10 --output_dir "$html_file.files_path" --output_html "$html_file"
11 #end if 11 #end if
12 #if $makeTAB.value=="yes": 12 #if $make_HTML.value=="yes":
13 --make_HTML "yes"
14 #end if
15 #if $make_TAB.value=="yes":
13 --output_tab "$tab_file" 16 --output_tab "$tab_file"
14 #end if 17 #end if
15 #if $makeTool.value=="yes": 18 #if $factory.make_Tool=="yes":
16 --makeTool "$makeTool" 19 --make_Tool "$factory.make_Tool"
20 --help_text "$helpme"
21 --tool_desc "$factory.tool_desc"
17 #end if 22 #end if
18 #end if 23 #end if
19 </command> 24 </command>
20 <inputs> 25 <inputs>
21 <param name="input1" type="data" format="tabular" label="Select an optional input tabular file from your history" optional="true" 26 <param name="input1" type="data" format="tabular" label="Select an optional input tabular file from your history" optional="true"
22 help="Your script probably needs an input - but if not, this can be left unassigned"/> 27 help="Your script probably needs an input - but if not, this can be left unassigned"/>
23 <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain"/> 28 <param name="tool_name" type="text" value="My dynamic script" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain"/>
24 <param name="makeTool" type="select" label="Create a tar.gz file ready for local toolshed entry" 29 <conditional name="factory">
25 help="Ready to deploy securely! with tests eventually"> 30 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!">
26 <option value="yes">Yes</option> 31 <option value="yes">Yes</option>
27 <option value="" selected="true">Not yet, it's still broken</option> 32 <option value="" selected="true">Not yet, it's still broken</option>
28 </param> 33 </param>
29 <param name="makeHTML" type="select" label="Create an HTML output with all script outputs collected together, with thumbnails of new PDF images, the script and a run log file" 34 <when value = "yes">
35 <param name="tool_desc" type="text" width="120" value="" help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
36 <param name="help_text" type="text" area="true" size="8x80" width="120" value="**What it Does**" help="Supply the brief user documentation to appear on the new tool form as reStructured text" >
37 <sanitizer>
38 <valid initial="string.printable">
39 </valid>
40 <mapping initial="none"/>
41 </sanitizer>
42 </param>
43 </when>
44 </conditional>
45 <param name="make_HTML" type="select" label="Create an HTML output with all script outputs collected together, with thumbnails of new PDF images, the script and a run log file"
30 help="This is useful for presenting complex outputs and is not needed if your script doesn't create anything other than a single tabular output"> 46 help="This is useful for presenting complex outputs and is not needed if your script doesn't create anything other than a single tabular output">
31 <option value="yes">Yes</option> 47 <option value="yes">Yes</option>
32 <option value="" selected="true">No</option> 48 <option value="" selected="true">No</option>
33 </param> 49 </param>
34 <param name="makeTAB" type="select" label="Create a new tabular history output" 50 <param name="make_TAB" type="select" label="Create a new tabular history output"
35 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> 51 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
36 <option value="yes" selected="true">Yes</option> 52 <option value="yes" selected="true">Yes</option>
37 <option value="">No</option> 53 <option value="">No</option>
38 </param> 54 </param>
39 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> 55 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
40 <option value="Rscript" selected="true">Rscript</option> 56 <option value="Rscript" selected="true">Rscript</option>
41 <option value="python">python</option> 57 <option value="python">python</option>
42 <option value="perl (ugh)">perl</option> 58 <option value="perl (ugh)">perl</option>
43 </param> 59 </param>
44 <param name="dynScript" label="Your Script Goes Here" type="text" value="" area="True" size="8x80" width="80" 60 <param name="dynScript" label="Your Script Goes Here" type="text" value="" area="True" size="8x80" width="80"
45 help="Expect FIRST CL parameter = the optional input tabular file path (or NONE if not specified). Ensure your script writes tabular output to the path in the SECOND command line parameter it gets."/> 61 help="Expect FIRST CL parameter = the optional input tabular file path (or NONE if not specified). Ensure your script writes tabular output to the path in the SECOND command line parameter it gets.">
62 <sanitizer>
63 <valid initial="string.printable">
64 </valid>
65 <mapping initial="none"/>
66 </sanitizer>
67 </param>
46 </inputs> 68 </inputs>
47 <outputs> 69 <outputs>
48 <data format="tabular" name="tab_file" label="${tool_name}.xls"> 70 <data format="tabular" name="tab_file" label="${tool_name}.xls">
49 <filter> makeTAB=="yes" </filter> 71 <filter> make_TAB=="yes" </filter>
50 </data> 72 </data>
51 <data format="html" name="html_file" label="${tool_name}.html"> 73 <data format="html" name="html_file" label="${tool_name}.html">
52 <filter> makeHTML=="yes" or makeTool=="yes"</filter> 74 <filter> make_HTML=="yes" or make_Tool=="yes"</filter>
53 </data> 75 </data>
54 </outputs> 76 </outputs>
55 <configfiles> 77 <configfiles>
56 <configfile name="runme"> 78 <configfile name="runme">
57 ${dynScript} 79 ${dynScript}
58 </configfile> 80 </configfile>
81 #if $factory.make_Tool == "yes":
82 <configfile name="helpme">
83 $factory.help_text
84 </configfile>
85 #end if
86
59 </configfiles> 87 </configfiles>
60 <help> 88 <help>
61 **What it does** 89 **What it does**
62 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy. 90 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
63 This is (extremely) insecure. 91 This is (extremely) insecure.