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annotate rgDynamicScriptWrapper.xml @ 4:3755b2365fb0

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author ross lazarus ross.lazarus@gmail.com
date Thu, 31 May 2012 09:49:38 +1000
parents fda8032fe989
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1 <tool id="rgDynamic1" name="Dynamic Script Runner" version="0.03">
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2 <description>DIY scripting</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 rgDynamicScriptWrapper.py --bad_user $__user_email__
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6 #else:
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7 rgDynamicScriptWrapper.py --script_path "$runme" --interpreter "$interpreter"
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8 --tool_name "$tool_name" --input_tab "$input1" --user_email "${__user_email__}"
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9 #if $makeHTML.value=="yes":
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10 --output_dir "$html_file.files_path" --output_html "$html_file"
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11 #end if
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12 #if $makeTAB.value=="yes":
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13 --output_tab "$tab_file"
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14 #end if
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15 #end if
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16 </command>
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17 <inputs>
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18 <param name="input1" type="data" format="tabular" label="Select an optional input tabular file from your history" optional="true"
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19 help="Your script probably needs an input - but if not, this can be left unassigned"/>
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20 <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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21 <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"
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22 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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23 <option value="yes">Yes</option>
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24 <option value="" selected="true">No</option>
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25 </param>
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26 <param name="makeTAB" type="select" label="Create a new tabular history output"
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27 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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28 <option value="yes" selected="true">Yes</option>
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29 <option value="">No</option>
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30 </param>
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31 <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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32 <option value="Rscript" selected="true">Rscript</option>
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33 <option value="python">python</option>
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34 <option value="perl (ugh)">perl</option>
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35 </param>
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36 <param name="dynScript" label="Your Script Goes Here" type="text" value="" area="True" size="8x80" width="80"
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37 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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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="tab_file" label="${tool_name}.xls">
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41 <filter> makeTAB=="yes" </filter>
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42 </data>
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43 <data format="html" name="html_file" label="${tool_name}.html">
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44 <filter> makeHTML=="yes" </filter>
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45 </data>
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46 </outputs>
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47 <configfiles>
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48 <configfile name="runme">
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49 ${dynScript}
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50 </configfile>
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51 </configfiles>
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52 <help>
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53 **What it does**
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54 This tool enables a user to paste and submit an arbitrary R/python/perl script to run in Galaxy.
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55 This is (extremely) insecure.
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56
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57 **Restrictions**
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58 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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59 Ask your friendly Galaxy administrator to edit this tool's source for you if you need this.
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60
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61 **Note to system administrators**
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62 Under no circumstances should you allow any user to use this tool unless you really, really trust them to do
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63 no harm.
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64
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65 **Use on public servers**
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66 is STRONGLY discouraged for obvious reasons
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67
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68 **Scripting conventions**
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69 The pasted script will be executed.
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70 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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71 as the first command line parameter
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72
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73 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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74 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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75 Any pdf images will automagically be converted to show thumbnails in that output.
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76 This can be handy for complex scripts creating lots of output.
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77
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78 **Simple Rscript example**
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79
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80 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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81
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82 ourargs = commandArgs(TRUE)
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83 inf = ourargs[1]
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84 outf = ourargs[2]
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85 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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86 inp[,5] = runif ( nrow(inp) )
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87 write.table(inp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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88
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89
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90 </help>
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91
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92 </tool>
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93
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94