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comparison rgToolFactory.xml @ 9:e09c76551bed

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Can run without input or output or either.. random heatmap (no inputs) example added to docs
author ross lazarus ross.lazarus@gmail.com
date Sat, 02 Jun 2012 21:08:57 +1000
parents 220885b2d7ee
children 71f2ac0eee95
comparison
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8:220885b2d7ee 9:e09c76551bed
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 "$input1" 8 --tool_name "$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
12 #if $input1.value != 'None':
13 --input_tab "$input1"
11 #end if 14 #end if
12 #if $make_HTML.value=="yes": 15 #if $make_HTML.value=="yes":
13 --make_HTML "yes" 16 --make_HTML "yes"
14 #end if 17 #end if
15 #if $make_TAB.value=="yes": 18 #if $make_TAB.value=="yes":
76 </outputs> 79 </outputs>
77 <configfiles> 80 <configfiles>
78 <configfile name="runme"> 81 <configfile name="runme">
79 ${dynScript} 82 ${dynScript}
80 </configfile> 83 </configfile>
84
85 <configfile name="helpme">
81 #if $factory.make_Tool == "yes": 86 #if $factory.make_Tool == "yes":
82 <configfile name="helpme">
83 $factory.help_text 87 $factory.help_text
88 #end if
84 </configfile> 89 </configfile>
85 #end if
86
87 </configfiles> 90 </configfiles>
88 <help> 91 <help>
89 **What it does** 92 **What it does**
90 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.
91 This is (extremely) insecure. 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.
92 97
93 **Restrictions** 98 **Restrictions**
94 This tool will ONLY work if your user id has been added to the local copy's list of permitted users. 99 This tool will ONLY work if your user id has been added to the local copy's list of permitted users.
95 Ask your friendly Galaxy administrator to edit this tool's source for you if you need this. 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
101 is authorised to use it - == it will not run otherwise ==
96 102
97 **Note to system administrators** 103 **Note to system administrators**
98 Under no circumstances should you allow any user to use this tool unless you really, really trust them to do 104 Under no circumstances should you allow any user to use this tool unless you really, really trust them to do
99 no harm. 105 no harm.
100 106
120 outf = ourargs[2] 126 outf = ourargs[2]
121 inp = read.table(inf,head=F,row.names=NULL,sep='\t') 127 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
122 outp = t(inp) 128 outp = t(inp)
123 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F) 129 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
124 130
131 A more complex example takes no input file but generates a random heatmap pdf - you must make sure the option to create an HTML output file is
132 turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
133
134 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
135 bar = as.matrix(foo)
136 pdf( "heattest.pdf" )
137 heatmap(bar,main='Random Heatmap')
138 dev.off()
139
140
125 </help> 141 </help>
126 142
127 </tool> 143 </tool>
128 144
129 145