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annotate rgToolFactory.xml @ 15:8594478e8d2c

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Silly typo from testing test generation
author Ross Lazarus <ross.lazarus@gmail.com>
date Mon, 04 Jun 2012 11:06:41 +1000
parents d12728e33c3d
children a87a262220a4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="rgTF" name="Tool Factory" version="0.05">
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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 ['rlazarus@bakeridi.edu.au','mziemann@bakeridi.edu.au','akaspi@bakeridi.edu.au'] ):
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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 $make_TAB.value=="yes":
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10 --output_tab "$tab_file"
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11 #end if
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12 #if $factory.make_Tool=="yes":
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13 --make_Tool "$factory.make_Tool"
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14 --help_text "$helpme"
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15 --tool_desc "$factory.tool_desc"
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16 --new_tool "$new_tool"
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17 #end if
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18 #if $make_HTML.value=="yes":
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19 --output_dir "$html_file.files_path" --output_html "$html_file"
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20 #end if
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21 #if $input1 != 'None':
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22 --input_tab "$input1"
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23 #end if
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24 #if $make_HTML.value=="yes":
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25 --make_HTML "yes"
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26 #end if
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27 #end if
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28 </command>
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29 <inputs>
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30 <param name="input1" type="data" label="Select an optional input file from your history" optional="true"
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31 help="Your script probably needs an input - but if not, this can be left unassigned. Note that your script MUST be able to parse whatever format you choose!"/>
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32 <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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33 <sanitizer>
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34 <valid initial="string.letters,string.digits">
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35 <mapping initial="none"/>
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36 </valid>
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37 </sanitizer>
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38 </param>
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39 <conditional name="factory">
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40 <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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41 <option value="yes">Yes</option>
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42 <option value="" selected="true">Not yet, it's still broken</option>
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43 </param>
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44 <when value = "yes">
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45 <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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46 <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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47 <sanitizer>
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48 <valid initial="string.printable">
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49 </valid>
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50 <mapping initial="none"/>
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51 </sanitizer>
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52 </param>
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53 </when>
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54 </conditional>
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55 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images"
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56 help="Recommended for presenting complex outputs in an accessible manner">
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57 <option value="yes">Yes</option>
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58 <option value="" selected="true">No</option>
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59 </param>
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60 <param name="make_TAB" type="select" label="Create a new tabular history output"
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61 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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62 <option value="yes" selected="true">Yes</option>
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63 <option value="">No</option>
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64 </param>
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65 <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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66 <option value="Rscript" selected="true">Rscript</option>
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67 <option value="python">python</option>
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68 <option value="perl (ugh)">perl</option>
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69 </param>
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70 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x80" width="80"
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71 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').">
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72 <sanitizer>
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73 <valid initial="string.printable">
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74 </valid>
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75 <mapping initial="none"/>
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76 </sanitizer>
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77 </param>
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78 </inputs>
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79 <outputs>
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80 <data format="tabular" name="tab_file" label="${tool_name}.xls">
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81 <filter>make_TAB == "yes"</filter>
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82 </data>
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83 <data format="html" name="html_file" label="${tool_name}.html">
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84 <filter>make_HTML == "yes"</filter>
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85 </data>
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86 <data format="gz" name="new_tool" label="${tool_name}_tool.gz">
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87 <filter>factory['make_Tool'] == "yes"</filter>
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88 </data>
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89 </outputs>
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90 <configfiles>
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91 <configfile name="runme">
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92 ${dynScript}
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93 </configfile>
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94
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95 <configfile name="helpme">
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96 #if $factory.make_Tool == "yes":
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97 ${factory.help_text}
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98 #end if
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99 </configfile>
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100 </configfiles>
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101 <help>
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102 **What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
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103
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104 **Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
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105
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106 **Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
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107 a new HTML report linking all the files and images created by the script can be automatically generated.
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108
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109 **Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
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110 ready to upload to your local toolshed for sharing and installation.
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111
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112 **Permission to to use this tool** must be explicitly granted by an administrator adding approved Galaxy user IDs to the local tool XML list of permitted users. *It will not run otherwise*
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113
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114 .. class:: warningmark
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115
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116 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts and should only be installed on private/personnal Galaxy instances.
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117 Under no circumstances should you allow any user to use this tool unless you really, really trust them with the power to do what they want as the Galaxy user.
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118
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119 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
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120
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121 .. class:: warningmark
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122
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123 **Use on public servers** is STRONGLY discouraged for obvious reasons
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124
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125 **Scripting conventions** The pasted script will be executed with the path to the (optional) input tabular data file path or NONE if you do not select one, and the path to the optional
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126 output file or None if none is wanted, as the first and second command line parameters. The script must deal appropriately with these - see Rscript examples below.
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127 Note that if an optional HTML output is selected, all the output files created by the script will be nicely presented as links, with pdf images linked as thumbnails in that output.
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128 This can be handy for complex scripts creating lots of output.
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129
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130 **Simple examples**
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131
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132 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and writes the results to a new tabular file::
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133
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134 # transpose a tabular input file and write as a tabular output file
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135 ourargs = commandArgs(TRUE)
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136 inf = ourargs[1]
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137 outf = ourargs[2]
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138 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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139 outp = t(inp)
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140 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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141
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142 A more complex Rscript 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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143 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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144
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145 # note this script takes NO input or output because it generates random data
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146 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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147 bar = as.matrix(foo)
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148 pdf( "heattest.pdf" )
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149 heatmap(bar,main='Random Heatmap')
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150 dev.off()
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151
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152 A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces for this to work if cut and pasted into the script box)::
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153
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154 # reverse order of columns in a tabular file
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155 import sys
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156 inp = sys.argv[1]
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157 outp = sys.argv[2]
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158 i = open(inp,'r')
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159 o = open(outp,'w')
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160 for row in i:
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161 rs = row.rstrip().split('\t')
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162 rs.reverse()
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163 o.write('\t'.join(rs))
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164 o.write('\n')
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165 i.close()
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166 o.close()
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167
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168
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169 **Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
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170
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171 All rights reserved.
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172
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173 Licensed under the LGPL_
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174
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175 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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176
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177 </help>
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178
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179 </tool>
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180
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181