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comparison rgToolFactory.xml @ 10:71f2ac0eee95

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Updated tarball with some test material - still need code generated... Completed a round trip test via a local toolshed. Awsome
author ross lazarus ross.lazarus@gmail.com
date Sat, 02 Jun 2012 22:40:33 +1000
parents e09c76551bed
children a0a5d0757e39
comparison
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9:e09c76551bed 10:71f2ac0eee95
7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
8 --tool_name "$tool_name" 8 --tool_name "$tool_name"
9 #if $make_HTML.value=="yes" or $factory.make_Tool=="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 $input1.value != 'None': 12 #if $input1 != 'None':
13 --input_tab "$input1" 13 --input_tab "$input1"
14 #end if 14 #end if
15 #if $make_HTML.value=="yes": 15 #if $make_HTML.value=="yes":
16 --make_HTML "yes" 16 --make_HTML "yes"
17 #end if 17 #end if
72 <outputs> 72 <outputs>
73 <data format="tabular" name="tab_file" label="${tool_name}.xls"> 73 <data format="tabular" name="tab_file" label="${tool_name}.xls">
74 <filter> make_TAB=="yes" </filter> 74 <filter> make_TAB=="yes" </filter>
75 </data> 75 </data>
76 <data format="html" name="html_file" label="${tool_name}.html"> 76 <data format="html" name="html_file" label="${tool_name}.html">
77 <filter> make_HTML=="yes" or make_Tool=="yes"</filter> 77 <filter>make_HTML=="yes" or factory.make_Tool=="yes"</filter>
78 </data> 78 </data>
79 </outputs> 79 </outputs>
80 <configfiles> 80 <configfiles>
81 <configfile name="runme"> 81 <configfile name="runme">
82 ${dynScript} 82 ${dynScript}
89 </configfile> 89 </configfile>
90 </configfiles> 90 </configfiles>
91 <help> 91 <help>
92 **What it does** 92 **What it does**
93 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy. 93 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
94 This is (extremely) insecure. However, once you get the script working on some test data, you can generate a complete ready to run
95 Galaxy tool by setting the "Make tool" option to Yes. The resulting tarball will be ready to install
96 It will run like as securely as any other Galaxy tool - unlike this one used to generate it.
97 94
98 **Restrictions** 95 **Restrictions**
99 This tool will ONLY work if your user id has been added to the local copy's list of permitted users. 96 This tool will ONLY work if your user id has been added to the local copy's list of permitted users.
100 It should only ever be used on a private, personal Galaxy instance and you should edit this tool's source so your local login 97 It should only ever be used on a private, personal Galaxy instance and you should edit this tool's source so your local login
101 is authorised to use it - == it will not run otherwise == 98 is authorised to use it - *it will not run otherwise*
102 99
103 **Note to system administrators** 100 .. class:: warningmark
104 Under no circumstances should you allow any user to use this tool unless you really, really trust them to do
105 no harm.
106 101
107 **Use on public servers** 102 **Note to system administrators** Under no circumstances should you allow any user to use this tool unless you really, really trust them to do
108 is STRONGLY discouraged for obvious reasons 103 no harm. This tool (extremely) insecure and is only recommended for private/personnal Galaxy instances.
104
105 Once you get the script working on some test data, you can generate a complete ready to run
106 Galaxy tool by setting the "Make tool" option to Yes. The resulting tarball will be ready to install
107 It will run just as securely as any other normal Galaxy tool - unlike this one used to generate it.
108
109 .. class:: warningmark
110
111 **Use on public servers** is STRONGLY discouraged for obvious reasons
109 112
110 **Scripting conventions** 113 **Scripting conventions**
111 The pasted script will be executed. 114 The pasted script will be executed.
112 It will get the path to the (optional) input tabular data file path or NONE if you do not select one 115 It will get the path to the (optional) input tabular data file path or NONE if you do not select one
113 as the first command line parameter 116 as the first command line parameter
135 bar = as.matrix(foo) 138 bar = as.matrix(foo)
136 pdf( "heattest.pdf" ) 139 pdf( "heattest.pdf" )
137 heatmap(bar,main='Random Heatmap') 140 heatmap(bar,main='Random Heatmap')
138 dev.off() 141 dev.off()
139 142
140 143 **Attribution**
144 Copyright ross lazarus (ross.lazarus at gmail stop com) May 2012
145 All rights reserved
146 Licensed under the LGPL for your pleasure
141 </help> 147 </help>
142 148
143 </tool> 149 </tool>
144 150
145 151