Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate 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
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1 <tool id="rgTF" name="Tool Factory" version="0.04">
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2 <description>Makes scripts into tools</description>
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3 <command interpreter="python">
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4 #if ( $__user_email__ not in ['ross.lazarus@gmail.com',] ):
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5 rgToolFactory.py --bad_user $__user_email__
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6 #else:
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7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
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8 --tool_name "$tool_name"
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9 #if $make_HTML.value=="yes" or $factory.make_Tool=="yes":
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10 --output_dir "$html_file.files_path" --output_html "$html_file"
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11 #end if
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12 #if $input1 != 'None':
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13 --input_tab "$input1"
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14 #end if
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15 #if $make_HTML.value=="yes":
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16 --make_HTML "yes"
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17 #end if
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18 #if $make_TAB.value=="yes":
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19 --output_tab "$tab_file"
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20 #end if
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21 #if $factory.make_Tool=="yes":
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22 --make_Tool "$factory.make_Tool"
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23 --help_text "$helpme"
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24 --tool_desc "$factory.tool_desc"
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25 #end if
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26 #end if
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27 </command>
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28 <inputs>
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29 <param name="input1" type="data" format="tabular" label="Select an optional input tabular file from your history" optional="true"
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30 help="Your script probably needs an input - but if not, this can be left unassigned"/>
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31 <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"/>
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32 <conditional name="factory">
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33 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!">
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34 <option value="yes">Yes</option>
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35 <option value="" selected="true">Not yet, it's still broken</option>
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36 </param>
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37 <when value = "yes">
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38 <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)" />
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39 <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" >
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 </valid>
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43 <mapping initial="none"/>
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44 </sanitizer>
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45 </param>
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46 </when>
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47 </conditional>
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48 <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"
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49 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">
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50 <option value="yes">Yes</option>
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51 <option value="" selected="true">No</option>
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52 </param>
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53 <param name="make_TAB" type="select" label="Create a new tabular history output"
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54 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
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55 <option value="yes" selected="true">Yes</option>
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56 <option value="">No</option>
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57 </param>
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58 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
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59 <option value="Rscript" selected="true">Rscript</option>
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60 <option value="python">python</option>
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61 <option value="perl (ugh)">perl</option>
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62 </param>
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63 <param name="dynScript" label="Your Script Goes Here" type="text" value="" area="True" size="8x80" width="80"
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64 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.">
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65 <sanitizer>
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66 <valid initial="string.printable">
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67 </valid>
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68 <mapping initial="none"/>
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69 </sanitizer>
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70 </param>
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71 </inputs>
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72 <outputs>
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73 <data format="tabular" name="tab_file" label="${tool_name}.xls">
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74 <filter> make_TAB=="yes" </filter>
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75 </data>
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76 <data format="html" name="html_file" label="${tool_name}.html">
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77 <filter>make_HTML=="yes" or factory.make_Tool=="yes"</filter>
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78 </data>
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79 </outputs>
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80 <configfiles>
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81 <configfile name="runme">
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82 ${dynScript}
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83 </configfile>
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84
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85 <configfile name="helpme">
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86 #if $factory.make_Tool == "yes":
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87 $factory.help_text
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88 #end if
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89 </configfile>
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90 </configfiles>
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91 <help>
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92 **What it does**
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93 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
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94
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95 **Restrictions**
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96 This tool will ONLY work if your user id has been added to the local copy's list of permitted users.
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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
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98 is authorised to use it - *it will not run otherwise*
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99
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100 .. class:: warningmark
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101
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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
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103 no harm. This tool (extremely) insecure and is only recommended for private/personnal Galaxy instances.
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104
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105 Once you get the script working on some test data, you can generate a complete ready to run
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106 Galaxy tool by setting the "Make tool" option to Yes. The resulting tarball will be ready to install
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107 It will run just as securely as any other normal Galaxy tool - unlike this one used to generate it.
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108
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109 .. class:: warningmark
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110
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111 **Use on public servers** is STRONGLY discouraged for obvious reasons
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112
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113 **Scripting conventions**
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114 The pasted script will be executed.
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115 It will get the path to the (optional) input tabular data file path or NONE if you do not select one
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116 as the first command line parameter
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117
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118 The script must write it's output as tab delimited text to the path found as the second command line parameter
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119 Note that if an optional HTML output is selected, all the output files spewed by your script will be nicely presented as links to the user.
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120 Any pdf images will automagically be converted to show thumbnails in that output.
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121 This can be handy for complex scripts creating lots of output.
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122
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123 **Simple Rscript example**
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124
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125 A simple "filter" that takes an input file, does something and writes the results to a new tabular file might look like this::
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126
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127 ourargs = commandArgs(TRUE)
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128 inf = ourargs[1]
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129 outf = ourargs[2]
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130 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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131 outp = t(inp)
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132 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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133
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134 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
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135 turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
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136
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137 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
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138 bar = as.matrix(foo)
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139 pdf( "heattest.pdf" )
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140 heatmap(bar,main='Random Heatmap')
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141 dev.off()
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142
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143 **Attribution**
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144 Copyright ross lazarus (ross.lazarus at gmail stop com) May 2012
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145 All rights reserved
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146 Licensed under the LGPL for your pleasure
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147 </help>
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148
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149 </tool>
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150
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151