skunkworks: rgToolFactoryMultIn.xml annotate

annotate rgToolFactoryMultIn.xml @ 30:fb3fa6a2874d draft

Citations added (thanks John!) and a few more output formats for Alistair Chilcott

author	fubar
date	Thu, 28 Aug 2014 02:22:39 -0400
parents
children

rev	line source
30 fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	1 <tool id="rgTFM" name="Tool Factory Multiple Inputs" version="1.12">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	2 <description>Makes scripts into tools</description>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	3 <requirements>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	4 <requirement type="package" version="9.10">ghostscript</requirement>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	5 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	6 </requirements>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	7 <command interpreter="python">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	8 #if ( $__user_email__ not in $__admin_users__ ):
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	9 rgToolFactoryMultIn.py --bad_user $__user_email__
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	10 #else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	11 rgToolFactoryMultIn.py --script_path "$runme" --interpreter "$interpreter"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	12 --tool_name "$tool_name" --user_email "$__user_email__"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	13 #if $make_TAB.value=="yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	14 --output_tab "$output1"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	15 --output_format "$output_format"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	16 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	17 #if $makeMode.make_Tool=="yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	18 --make_Tool "$makeMode.make_Tool"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	19 --tool_desc "$makeMode.tool_desc"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	20 --tool_version "$makeMode.tool_version"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	21 --new_tool "$new_tool"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	22 --help_text "$helpme"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	23 #if $make_HTML.value=="yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	24 #if $makeMode.include_deps.value=="yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	25 --include_dependencies "yes"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	26 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	27 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	28 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	29 #if $make_HTML.value=="yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	30 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	31 #else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	32 --output_dir "."
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	33 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	34 #if $input1 != 'None':
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	35 --input_formats "$input_formats"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	36 #for intab in $input1:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	37 #if $add_names.value == "yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	38 --input_tab "$intab,$intab.name"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	39 #else:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	40 --input_tab "$intab"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	41 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	42 #end for
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	43 --input_formats = "$input_formats"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	44 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	45 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	46 </command>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	47 <inputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	48 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120" multiple="true"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	49 help="Use the multiple input widget (above/right of input box) for multiple inputs - your script MUST be ready to parse the command line right - see samples below"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	50 <param name="input_formats" type="text" value="tabular" label="Select allowable Galaxy input formats for your inputs passed to your script - default is tabular"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	51 help="Multiple input formats are allowed as a comma separated list (eg 'tabular,txt'), but your script must be able to deal with whatever is passed in!">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	52 <sanitizer invalid_char="">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	53 <valid initial="string.letters">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	54 <add value=","/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	55 <add value=" "/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	56 </valid>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	57 </sanitizer>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	58 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	59 <param name="add_names" type="select" label="Pass input file(s) as path,name - useful if you need the user supplied Galaxy name for your data sets"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	60 help="Your script is responsible for parsing and dealing with these comma separated values!">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	61 <option value="yes">Pass inputs as comma separated path,name values on the script command line</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	62 <option value="" selected="true">Pass input parameters as path only - do not include the user supplied name</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	63 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	64 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	65 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	66 <sanitizer invalid_char="">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	67 <valid initial="string.letters,string.digits">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	68 <add value="_"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	69 </valid>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	70 </sanitizer>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	71 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	72 <conditional name="makeMode">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	73 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	74 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	75 <option value="" selected="true">No. Just run the script please</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	76 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	77 <when value = "yes">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	78 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	79 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	80 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	81 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	82 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	83 size="8x120" value="What it Does"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	84 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" >
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	85 <sanitizer>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	86 <valid initial="string.printable">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	87 </valid>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	88 <mapping initial="none"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	89 </sanitizer>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	90 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	91 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	92 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	93 <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	94 <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	95 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	96
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	97 </when>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	98 <when value = "">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	99 </when>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	100 </conditional>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	101 <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"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	102 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	103 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	104 <option value="" selected="true">No, no HTML output file thanks</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	105 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	106 <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	107 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	108 <option value="yes" selected="true">My script writes to a new history output</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	109 <option value="">I do not want a new history output file</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	110 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	111 <param name="output_format" type="select" label="Galaxy datatype for your tool's output file if any" help="You may need to edit the xml to extend this list">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	112 <option value="tabular" selected="true">Tabular</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	113 <option value="text">text</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	114 <option value="interval">Interval</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	115 <option value="gz">gz</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	116 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	117 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	118 <option value="Rscript" selected="true">Rscript</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	119 <option value="python">python</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	120 <option value="perl">perl</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	121 <option value="sh">sh</option>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	122 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	123 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	124 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').">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	125 <sanitizer>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	126 <valid initial="string.printable">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	127 </valid>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	128 <mapping initial="none"/>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	129 </sanitizer>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	130 </param>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	131 </inputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	132 <outputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	133 <data format="tabular" name="output1" label="${tool_name}.${output_format}">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	134 <filter>make_TAB=="yes"</filter>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	135 <change_format>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	136 <when input="output_format" value="interval" format="interval" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	137 <when input="output_format" value="gz" format="gz" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	138 <when input="output_format" value="text" format="text" />
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	139 </change_format>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	140 </data>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	141 <data format="html" name="html_file" label="${tool_name}.html">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	142 <filter>make_HTML == "yes"</filter>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	143 </data>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	144 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	145 <filter>makeMode['make_Tool'] == "yes"</filter>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	146 </data>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	147 </outputs>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	148 <configfiles>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	149 <configfile name="runme">$dynScript</configfile>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	150 <configfile name="helpme">
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	151 #if $makeMode.make_Tool == "yes":
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	152 ${makeMode.help_text}
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	153 #end if
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	154 </configfile>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	155 </configfiles>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	156 <help>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	157
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	158 .. class:: warningmark
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	159
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	160 Details and attribution GTF_
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	161
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	162 Local Admins ONLY Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	163
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	164 If you find a bug please raise an issue at the bitbucket repository GTFI_
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	165
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	166 What it does This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	167
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	168 Input options This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	169
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	170 Output options Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	171 a new HTML report linking all the files and images created by the script can be automatically generated.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	172
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	173 Tool Generation option Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	174 ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	175 it will become the input for the generated functional test.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	176
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	177 .. class:: warningmark
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	178
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	179 Note to system administrators This tool offers NO built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	180 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	181
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	182 .. class:: warningmark
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	183
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	184 Use on public servers is STRONGLY discouraged for obvious reasons
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	185
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	186 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.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	187 We recommend that you follow the good code hygiene practices associated with safe toolshed.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	188
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	189 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
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	190 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.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	191 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.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	192 This can be handy for complex scripts creating lots of output.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	193
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	194 Examples
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	195 <![CDATA[
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	196
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	197 Each of these following trivial examples can be cut and pasted into the script box for testing.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	198 Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	199
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	200 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	201 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
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	202 as a string::
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	203
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	204 # transpose a tabular input file and write as a tabular output file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	205 ourargs = commandArgs(TRUE)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	206 inf = ourargs[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	207 outf = ourargs[2]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	208 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	209 outp = t(inp)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	210 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	211
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	212 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
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	213 given input file type(s) specified when the tool is generated ::
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	214
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	215 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	216 column = 1 # adjust if necessary for some other kind of input
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	217 ourargs = commandArgs(TRUE)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	218 inf = ourargs[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	219 outf = ourargs[2]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	220 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	221 p = inp[,column]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	222 q = p.adjust(p,method='BH')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	223 outp = cbind(inp,'BH Adjusted p-value'=q)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	224 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	225
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	226
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	227 A demonstration Rscript example takes no input file but generates some random data based pdf images
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	228 You must make sure the option to create an HTML output file is
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	229 turned on for this to work. Images (pdf) are linked via thumbnails and
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	230 all files have a link on the resulting HTML page::
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	231
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	232 # note this script takes NO input or output because it generates random data
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	233 for (i in 1:10) {
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	234 foo = runif(100)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	235 bar = rnorm(100)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	236 bar = foo + 0.05*bar
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	237 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	238 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	239 dev.off()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	240 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	241 bar = as.matrix(foo)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	242 pdf(paste('yet',i,"anotherheatmap.pdf",sep='_'))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	243 heatmap(bar,main='Random Heatmap')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	244 dev.off()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	245 }
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	246
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	247 A slight variation taking an input tabular file from which we read the first number as nreps
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	248
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	249 # note this script takes a single parameter
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	250 # number of replicates
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	251 ourargs = commandArgs(TRUE)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	252 infname = ourargs[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	253 nreps = read.table(infname,head=F)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	254 nreps = unlist(nreps)[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	255 nreps = max(c(1,nreps))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	256 nreps = min(c(20,nreps))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	257 print(paste("Using nreps=",nreps))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	258 for (i in 1:nreps) {
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	259 foo = runif(100)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	260 bar = rnorm(100)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	261 bar = foo + 0.2*bar
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	262 pdf(paste("yet",i,"anotherplot.pdf",sep="_"))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	263 plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	264 dev.off()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	265 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	266 bar = as.matrix(foo)
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	267 pdf(paste("yet",i,"anotherheatmap.pdf",sep="_"))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	268 heatmap(bar,main="Random Heatmap")
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	269 dev.off()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	270 }
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	271
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	272 A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	273 for this to work if cut and pasted into the script box)::
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	274
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	275 # reverse order of columns in a tabular file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	276 import sys
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	277 inp = sys.argv[1]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	278 outp = sys.argv[2]
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	279 i = open(inp,'r')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	280 o = open(outp,'w')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	281 for row in i:
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	282 rs = row.rstrip().split('\t')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	283 rs.reverse()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	284 o.write('\t'.join(rs))
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	285 o.write('\n')
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	286 i.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	287 o.close()
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	288
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	289 A trivial shell script example to show that it works::
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	290
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	291 #!/bin/bash
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	292 INF=$1
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	293 OUTF=$2
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	294 cut -c2,4,6,8,10,12 $INF > $OUTF
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	295
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	296 A trivial perl script example to show that even perl works::
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	297
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	298 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	299 # change all occurances of a string in a file to another string
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	300 #
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	301 $oldfile = $ARGV[0];
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	302 $newfile = $ARGV[1];
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	303 $old = "gene";
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	304 $new = "foo";
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	305 open(OF, $oldfile);
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	306 open(NF, ">$newfile");
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	307 # read in each line of the file
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	308 while ($line = <OF>) {
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	309 $line =~ s/$old/$new/;
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	310 print NF $line;
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	311 }
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	312 close(OF);
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	313 close(NF);
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	314
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	315 ]]>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	316
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	317 Citation
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	318
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	319
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	320 Paper_ :
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	321
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	322 Creating re-usable tools from scripts: The Galaxy Tool Factory
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	323 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	324 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	325
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	326
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	327 Licensing
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	328
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	329 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	330 All rights reserved.
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	331 Licensed under the LGPL_
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	332
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	333 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	334 .. _GTF: https://bitbucket.org/fubar/galaxytoolfactory
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	335 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	336 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	337
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	338
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	339 </help>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	340
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	341 </tool>
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	342
fb3fa6a2874d Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	343

Mercurial > repos > fubar > toolfactory

annotate rgToolFactoryMultIn.xml @ 30:fb3fa6a2874d draft