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annotate fubar-galaxytoolfactory-58871556de57/rgToolFactory.xml @ 6:cb4937b0c21d draft

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This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
author fubar
date Sun, 24 Feb 2013 17:15:29 -0500
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6
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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1 <tool id="rgTF" name="Tool Factory" version="0.10">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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2 <description>Makes scripts into tools</description>
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3 <command interpreter="python">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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4 #if ( $__user_email__ not in $__admin_users__ ):
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5 rgToolFactory.py --bad_user $__user_email__
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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6 #else:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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8 --tool_name "$tool_name" --user_email "$__user_email__"
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9 #if $make_TAB.value=="yes":
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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10 --output_tab "$tab_file"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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11 #end if
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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12 #if $makeMode.make_Tool=="yes":
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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13 --make_Tool "$makeMode.make_Tool"
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14 --tool_desc "$makeMode.tool_desc"
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15 --tool_version "$makeMode.tool_version"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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16 --new_tool "$new_tool"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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17 --help_text "$helpme"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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18 #end if
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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19 #if $make_HTML.value=="yes":
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20 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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21 #end if
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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22 #if $input1 != 'None':
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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23 --input_tab "$input1"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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24 #end if
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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25 #end if
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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26 </command>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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27 <inputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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28 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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29 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
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30 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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31 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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32 <sanitizer invalid_char="">
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33 <valid initial="string.letters,string.digits"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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34 </sanitizer>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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35 </param>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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36 <conditional name="makeMode">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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37 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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38 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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39 <option value="" selected="true">No. Just run the script please</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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40 </param>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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41 <when value = "yes">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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42 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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43 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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44 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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45 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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46 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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47 size="8x120" value="**What it Does**"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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48 help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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49 <sanitizer>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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50 <valid initial="string.printable">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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51 </valid>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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52 <mapping initial="none"/>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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53 </sanitizer>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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54 </param>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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55 </when>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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56 <when value = "">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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57 </when>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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58 </conditional>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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59 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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60 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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61 <option value="yes">Yes, arrange all outputs in an HTML output</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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62 <option value="" selected="true">No, no HTML output file thanks</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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63 </param>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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64
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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65
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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66 <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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67 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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68 <option value="yes" selected="true">My script writes to a new history output</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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69 <option value="">I only want an HTML output file</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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70 </param>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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71 <param name="out_format" type="select" label="Galaxy datatype for your tool's output file" help="You may need to edit the xml to extend this list">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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72 <option value="tabular" selected="true">Tabular</option>
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73 <option value="interval">Interval</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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74 <option value="gz">gz</option>
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75 <option value="text">text</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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76 </param>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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77 <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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78 <option value="Rscript" selected="true">Rscript</option>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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79 <option value="python">python</option>
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80 <option value="perl">perl</option>
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81 <option value="sh">sh</option>
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82 </param>
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83 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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84 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').">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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85 <sanitizer>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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86 <valid initial="string.printable">
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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87 </valid>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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88 <mapping initial="none"/>
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89 </sanitizer>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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90 </param>
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91 </inputs>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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92 <outputs>
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93 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
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94 <filter>make_TAB=="yes"</filter>
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95 <change_format>
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96 <when input="out_format" value="interval" format="interval" />
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97 <when input="out_format" value="gz" format="gz" />
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98 <when input="out_format" value="text" format="text" />
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99 </change_format>
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100 </data>
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101 <data format="html" name="html_file" label="${tool_name}.html">
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102 <filter>make_HTML == "yes"</filter>
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103 </data>
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104 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
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105 <filter>makeMode['make_Tool'] == "yes"</filter>
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106 </data>
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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107 </outputs>
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108 <configfiles>
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109 <configfile name="runme">$dynScript</configfile>
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110 <configfile name="helpme">
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111 #if $makeMode.make_Tool == "yes":
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112 ${makeMode.help_text}
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113 #end if
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114 </configfile>
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115 </configfiles>
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116 <help>
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117
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118 .. class:: warningmark
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119
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120 **Details and attribution** GTF_
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121
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122 **Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
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123
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124 **If you find a bug** please raise an issue at the bitbucket repository GTFI_
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125
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126 **What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
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127
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128 **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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129
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130 **Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
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131 a new HTML report linking all the files and images created by the script can be automatically generated.
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132
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133 **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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134 ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
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135 it will become the input for the generated functional test.
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136
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137 .. class:: warningmark
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138
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139 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
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140 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
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141
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142 .. class:: warningmark
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143
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144 **Use on public servers** is STRONGLY discouraged for obvious reasons
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145
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146 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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147 We recommend that you follow the good code hygiene practices associated with safe toolshed.
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148
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149 **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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150 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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151 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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152 This can be handy for complex scripts creating lots of output.
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153
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154 **Examples**
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155 <![CDATA[
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156
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157 Each of these following trivial examples can be cut and pasted into the script box for testing.
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158 Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input
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159
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160 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and
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161 writes the results to a new tabular file. Note the use of colClasses to ensure that no fiddling takes place with numeric values by treating everything
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162 as a string::
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163
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164 # transpose a tabular input file and write as a tabular output file
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165 ourargs = commandArgs(TRUE)
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166 inf = ourargs[1]
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167 outf = ourargs[2]
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168 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
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169 outp = t(inp)
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170 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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171
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172 Calculate a multiple test adjusted p value from a column of p values - for this script to be useful, it needs the right column for the input to be specified in the code for the
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173 given input file type(s) specified when the tool is generated ::
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174
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175 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
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176 column = 1 # adjust if necessary for some other kind of input
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177 ourargs = commandArgs(TRUE)
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178 inf = ourargs[1]
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179 outf = ourargs[2]
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180 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
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181 p = inp[,column]
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182 q = p.adjust(p,method='BH')
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183 outp = cbind(inp,'BH Adjusted p-value'=q)
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184 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
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185
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186
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187 A demonstration Rscript example takes no input file but generates some random data based pdf images
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188 You must make sure the option to create an HTML output file is
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189 turned on for this to work. Images (pdf) are linked via thumbnails and
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190 all files have a link on the resulting HTML page::
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191
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192 # note this script takes NO input or output because it generates random data
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193 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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194 bar = as.matrix(foo)
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195 pdf( "heattest.pdf" )
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196 heatmap(bar,main='Random Heatmap')
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197 dev.off()
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198 for (i in 1:49) {
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199 foo = runif(100)
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200 bar = rnorm(100)
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201 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
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202 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
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203 dev.off()
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204 }
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205
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206 A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
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207 for this to work if cut and pasted into the script box)::
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208
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209 # reverse order of columns in a tabular file
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210 import sys
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211 inp = sys.argv[1]
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212 outp = sys.argv[2]
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213 i = open(inp,'r')
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214 o = open(outp,'w')
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215 for row in i:
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216 rs = row.rstrip().split('\t')
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217 rs.reverse()
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218 o.write('\t'.join(rs))
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219 o.write('\n')
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220 i.close()
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221 o.close()
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222
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223 A trivial shell script example to show that it works::
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224
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225 #!/bin/bash
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226 INF=$1
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227 OUTF=$2
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228 cut -c2,4,6,8,10,12 $INF > $OUTF
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229
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230 A trivial perl script example to show that even perl works::
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231
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232 #
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233 # change all occurances of a string in a file to another string
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234 #
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235 $oldfile = $ARGV[0];
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236 $newfile = $ARGV[1];
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237 $old = "gene";
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238 $new = "foo";
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239 open(OF, $oldfile);
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240 open(NF, ">$newfile");
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241 # read in each line of the file
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242 while ($line = <OF>) {
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243 $line =~ s/$old/$new/;
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244 print NF $line;
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245 }
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246 close(OF);
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247 close(NF);
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248
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249 ]]>
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250
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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251 **Citation**
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252
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253
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254 Paper_ :
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255
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256 Creating re-usable tools from scripts: The Galaxy Tool Factory
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257 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
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258 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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259
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260
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261 **Licensing**
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262
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263 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
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264 All rights reserved.
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265 Licensed under the LGPL_
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266
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267 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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268 .. _GTF: https://bitbucket.org/fubar/galaxytoolfactory
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269 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues
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270 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref
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271
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272
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273 </help>
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274
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275 </tool>
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276
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277