skunkworks: fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.xml annotate

annotate fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.xml @ 2:b55b59435fb1 draft

Now with bash working I think. Special case but working..

author	fubar
date	Mon, 13 Aug 2012 06:27:26 -0400
parents
children

rev	line source
2 b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	1 <tool id="rgTF" name="Tool Factory" version="0.09">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	2 <description>Makes scripts into tools</description>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	3 <command interpreter="python">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	4 #if ( $__user_email__ not in $__admin_users__ ):
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	5 rgToolFactory.py --bad_user $__user_email__
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	6 #else:
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	8 --tool_name "$tool_name" --user_email "$__user_email__"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	9 #if $make_TAB.value=="yes":
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	10 --output_tab "$tab_file"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	11 #end if
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	12 #if $makeMode.make_Tool=="yes":
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	13 --make_Tool "$makeMode.make_Tool"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	14 --tool_desc "$makeMode.tool_desc"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	15 --tool_version "$makeMode.tool_version"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	16 --new_tool "$new_tool"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	17 --help_text "$helpme"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	18 #end if
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	19 #if $make_HTML.value=="yes":
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	20 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	21 #end if
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	22 #if $input1 != 'None':
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	23 --input_tab "$input1"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	24 #end if
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	25 #end if
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	26 </command>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	27 <inputs>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	28 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	29 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	30 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	31 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	32 <sanitizer invalid_char="">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	33 <valid initial="string.letters,string.digits"/>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	34 </sanitizer>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	35 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	36 <conditional name="makeMode">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	38 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	39 <option value="" selected="true">No. Just run the script please</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	40 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	41 <when value = "yes">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	42 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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"/>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	44 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	45 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	46 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	47 size="8x120" value="What it Does"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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" >
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	49 <sanitizer>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	50 <valid initial="string.printable">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	51 </valid>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	52 <mapping initial="none"/>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	53 </sanitizer>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	54 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	55 </when>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	56 <when value = "">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	57 </when>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	58 </conditional>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	60 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	61 <option value="yes">Yes, arrange all outputs in an HTML output</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	62 <option value="" selected="true">No, no HTML output file thanks</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	63 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	64
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	65
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	66 <param name="make_TAB" type="select" label="Create a new (default tabular) history output"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	68 <option value="yes" selected="true">My script writes to a new history output</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	69 <option value="">I only want an HTML output file</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	70 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	72 <option value="tabular" selected="true">Tabular</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	73 <option value="interval">Interval</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	74 <option value="gz">gz</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	75 <option value="text">text</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	76 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	77 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	78 <option value="Rscript" selected="true">Rscript</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	79 <option value="python">python</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	80 <option value="perl">perl</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	81 <option value="sh">sh</option>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	82 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	83 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	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').">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	85 <sanitizer>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	86 <valid initial="string.printable">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	87 </valid>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	88 <mapping initial="none"/>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	89 </sanitizer>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	90 </param>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	91 </inputs>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	92 <outputs>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	93 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	94 <filter>make_TAB=="yes"</filter>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	95 <change_format>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	96 <when input="out_format" value="interval" format="interval" />
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	97 <when input="out_format" value="gz" format="gz" />
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	98 <when input="out_format" value="text" format="text" />
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	99 </change_format>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	100 </data>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	101 <data format="html" name="html_file" label="${tool_name}.html">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	102 <filter>make_HTML == "yes"</filter>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	103 </data>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	104 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	105 <filter>makeMode['make_Tool'] == "yes"</filter>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	106 </data>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	107 </outputs>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	108 <configfiles>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	109 <configfile name="runme">$dynScript</configfile>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	110 <configfile name="helpme">
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	111 #if $makeMode.make_Tool == "yes":
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	112 ${makeMode.help_text}
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	113 #end if
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	114 </configfile>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	115 </configfiles>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	116 <help>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	117
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	118 .. class:: warningmark
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	119
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	120 Local Admins ONLY Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	121
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	122 What it does This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	123
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	124 Input options This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	125
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	126 Output options Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	127 a new HTML report linking all the files and images created by the script can be automatically generated.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	128
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	129 Tool Generation option Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	130 ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	131 it will become the input for the generated functional test.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	132
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	133 .. class:: warningmark
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	134
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	135 Note to system administrators This tool offers NO built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	136 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	137
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	138 .. class:: warningmark
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	139
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	140 Use on public servers is STRONGLY discouraged for obvious reasons
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	141
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	142 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.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	143 We recommend that you follow the good code hygiene practices associated with safe toolshed.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	144
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	145 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
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	146 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.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	147 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.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	148 This can be handy for complex scripts creating lots of output.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	149
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	150 Simple examples
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	151
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	152 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and writes the results to a new tabular file::
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	153
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	154 # transpose a tabular input file and write as a tabular output file
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	155 ourargs = commandArgs(TRUE)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	156 inf = ourargs[1]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	157 outf = ourargs[2]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	158 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	159 outp = t(inp)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	160 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	161
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	162 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
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	163 given input file type(s) specified when the tool is generated ::
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	164
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	165 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	166 column = 1 # adjust if necessary for some other kind of input
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	167 ourargs = commandArgs(TRUE)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	168 inf = ourargs[1]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	169 outf = ourargs[2]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	170 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	171 p = inp[,column]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	172 q = p.adjust(p,method='BH')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	173 outp = cbind(inp,'BH Adjusted p-value'=q)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	174 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	175
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	176
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	177 A demonstration Rscript example takes no input file but generates some random data based pdf images
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	178 You must make sure the option to create an HTML output file is
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	179 turned on for this to work. Images (pdf) are linked via thumbnails and
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	180 all files have a link on the resulting HTML page::
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	181
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	182 # note this script takes NO input or output because it generates random data
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	183 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	184 bar = as.matrix(foo)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	185 pdf( "heattest.pdf" )
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	186 heatmap(bar,main='Random Heatmap')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	187 dev.off()
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	188 for (i in 1:49) {
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	189 foo = runif(100)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	190 bar = rnorm(100)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	191 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	192 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	193 dev.off()
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	194 }
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	195
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	196 A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	197 for this to work if cut and pasted into the script box)::
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	198
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	199 # reverse order of columns in a tabular file
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	200 import sys
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	201 inp = sys.argv[1]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	202 outp = sys.argv[2]
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	203 i = open(inp,'r')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	204 o = open(outp,'w')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	205 for row in i:
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	206 rs = row.rstrip().split('\t')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	207 rs.reverse()
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	208 o.write('\t'.join(rs))
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	209 o.write('\n')
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	210 i.close()
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	211 o.close()
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	212
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	213 A trivial shell script example to show that it works::
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	214
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	215 #!/bin/bash
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	216 INF=$1
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	217 OUTF=$2
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	218 cut -c2,4,6,8,10,12 $INF >$OUTF
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	219
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	220
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	221 Attribution Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	222
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	223 All rights reserved.
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	224
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	225 Licensed under the LGPL_
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	226
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	227 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	228
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	229 </help>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	230
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	231 </tool>
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	232
b55b59435fb1 Now with bash working I think. Special case but working.. fubar parents: diff changeset	233

Mercurial > repos > fubar > toolfactory

annotate fubar-galaxytoolfactory-2e68c2a22b43/rgToolFactory.xml @ 2:b55b59435fb1 draft