skunkworks: rgToolFactory.xml annotate

annotate rgToolFactory.xml @ 24:f87139fe5e09 draft

fix for py script parsing

author	fubar
date	Sun, 27 Jul 2014 22:41:41 -0400
parents	8aab0f66cd5f
children

rev	line source
9 e4e097a41064 Uploaded fubar parents: 8 diff changeset	1 <tool id="rgTF" name="Tool Factory" version="1.10">
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	2 <description>Makes scripts into tools</description>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	3 <requirements>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	4 <requirement type="package" version="9.10">ghostscript</requirement>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	5 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	6 </requirements>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	7 <command interpreter="python">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	8 #if ( $__user_email__ not in $__admin_users__ ):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	9 rgToolFactory.py --bad_user $__user_email__
16 e052aadae3e9 Uploaded fubar parents: 10 diff changeset	10 #else:
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	11 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	12 --tool_name "$tool_name" --user_email "$__user_email__"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	13 #if $make_TAB.value=="yes":
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	14 --output_tab "$tab_file"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	15 #end if
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	16 #if $makeMode.make_Tool=="yes":
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	17 --make_Tool "$makeMode.make_Tool"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	18 --tool_desc "$makeMode.tool_desc"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	19 --tool_version "$makeMode.tool_version"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	20 --new_tool "$new_tool"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	21 --help_text "$helpme"
23 8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	22 #if $make_HTML.value=="yes":
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	23 --include_dependencies "${makeMode.include_deps}"
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	24 #end if
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	25 #end if
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	26 #if $make_HTML.value=="yes":
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	27 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
16 e052aadae3e9 Uploaded fubar parents: 10 diff changeset	28 #else:
e052aadae3e9 Uploaded fubar parents: 10 diff changeset	29 --output_dir "."
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	30 #end if
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	31 #if $input1 != 'None':
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	32 --input_tab "$input1"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	33 #end if
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	34 #end if
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	35 </command>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	36 <inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	37 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	38 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	39 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	40 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	41 <sanitizer invalid_char="">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	42 <valid initial="string.letters,string.digits"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	43 </sanitizer>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	44 </param>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	45 <conditional name="makeMode">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	46 <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry" help="Ready to deploy securely!" size="60">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	47 <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	48 <option value="" selected="true">No. Just run the script please</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	49 </param>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	50 <when value = "yes">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	51 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	52 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	53 <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	54 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	55 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	56 size="8x120" value="What it Does"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	57 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" >
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	58 <sanitizer>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	59 <valid initial="string.printable">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	60 </valid>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	61 <mapping initial="none"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	62 </sanitizer>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	63 </param>
23 8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	64 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	65 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	66 <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	67 <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	68 </param>
8aab0f66cd5f Uploaded fubar parents: 16 diff changeset	69
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	70 </when>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	71 <when value = "">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	72 </when>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	73 </conditional>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	74 <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"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	75 help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
9 e4e097a41064 Uploaded fubar parents: 8 diff changeset	76 <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	77 <option value="" selected="true">No, no HTML output file thanks</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	78 </param>
9 e4e097a41064 Uploaded fubar parents: 8 diff changeset	79 <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above"
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	80 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	81 <option value="yes" selected="true">My script writes to a new history output</option>
9 e4e097a41064 Uploaded fubar parents: 8 diff changeset	82 <option value="">I do not want a new history output file</option>
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	83 </param>
9 e4e097a41064 Uploaded fubar parents: 8 diff changeset	84 <param name="out_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">
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	85 <option value="tabular" selected="true">Tabular</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	86 <option value="interval">Interval</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	87 <option value="gz">gz</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	88 <option value="text">text</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	89 </param>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	90 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	91 <option value="Rscript" selected="true">Rscript</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	92 <option value="python">python</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	93 <option value="perl">perl</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	94 <option value="sh">sh</option>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	95 </param>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	96 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	97 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').">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	98 <sanitizer>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	99 <valid initial="string.printable">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	100 </valid>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	101 <mapping initial="none"/>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	102 </sanitizer>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	103 </param>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	104 </inputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	105 <outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	106 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	107 <filter>make_TAB=="yes"</filter>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	108 <change_format>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	109 <when input="out_format" value="interval" format="interval" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	110 <when input="out_format" value="gz" format="gz" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	111 <when input="out_format" value="text" format="text" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	112 </change_format>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	113 </data>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	114 <data format="html" name="html_file" label="${tool_name}.html">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	115 <filter>make_HTML == "yes"</filter>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	116 </data>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	117 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	118 <filter>makeMode['make_Tool'] == "yes"</filter>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	119 </data>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	120 </outputs>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	121 <configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	122 <configfile name="runme">$dynScript</configfile>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	123 <configfile name="helpme">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	124 #if $makeMode.make_Tool == "yes":
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	125 ${makeMode.help_text}
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	126 #end if
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	127 </configfile>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	128 </configfiles>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	129 <help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	130
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	131 .. class:: warningmark
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	132
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	133 Details and attribution GTF_
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	134
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	135 Local Admins ONLY Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	136
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	137 If you find a bug please raise an issue at the bitbucket repository GTFI_
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	138
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	139 What it does This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	140
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	141 Input options This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	142
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	143 Output options Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	144 a new HTML report linking all the files and images created by the script can be automatically generated.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	145
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	146 Tool Generation option Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	147 ready to upload to your local toolshed for sharing and installation. Provide a small sample input when you run generate the tool because
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	148 it will become the input for the generated functional test.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	149
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	150 .. class:: warningmark
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	151
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	152 Note to system administrators This tool offers NO built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	153 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	154
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	155 .. class:: warningmark
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	156
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	157 Use on public servers is STRONGLY discouraged for obvious reasons
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	158
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	159 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.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	160 We recommend that you follow the good code hygiene practices associated with safe toolshed.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	161
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	162 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
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	163 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.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	164 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.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	165 This can be handy for complex scripts creating lots of output.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	166
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	167 Examples
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	168 <![CDATA[
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	169
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	170 Each of these following trivial examples can be cut and pasted into the script box for testing.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	171 Please make sure you choose the appropriate interpreter and upload and select a suitable small matching test data input
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	172
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	173 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file, does something (transpose in this case) and
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	174 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
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	175 as a string::
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	176
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	177 # transpose a tabular input file and write as a tabular output file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	178 ourargs = commandArgs(TRUE)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	179 inf = ourargs[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	180 outf = ourargs[2]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	181 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	182 outp = t(inp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	183 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	184
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	185 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
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	186 given input file type(s) specified when the tool is generated ::
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	187
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	188 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	189 column = 1 # adjust if necessary for some other kind of input
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	190 ourargs = commandArgs(TRUE)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	191 inf = ourargs[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	192 outf = ourargs[2]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	193 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	194 p = inp[,column]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	195 q = p.adjust(p,method='BH')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	196 outp = cbind(inp,'BH Adjusted p-value'=q)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	197 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	198
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	199
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	200 A demonstration Rscript example takes no input file but generates some random data based pdf images
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	201 You must make sure the option to create an HTML output file is
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	202 turned on for this to work. Images (pdf) are linked via thumbnails and
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	203 all files have a link on the resulting HTML page::
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	204
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	205 # note this script takes NO input or output because it generates random data
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	206 for (i in 1:10) {
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	207 foo = runif(100)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	208 bar = rnorm(100)
10 59bce2efadfe Uploaded fubar parents: 9 diff changeset	209 bar = foo + 0.05*bar
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	210 pdf(paste('yet',i,"anotherplot.pdf",sep='_'))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	211 plot(foo,bar,main=paste("Foo by Bar plot #",i),col="maroon", pch=3,cex=0.6)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	212 dev.off()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	213 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	214 bar = as.matrix(foo)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	215 pdf(paste('yet',i,"anotherheatmap.pdf",sep='_'))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	216 heatmap(bar,main='Random Heatmap')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	217 dev.off()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	218 }
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	219
10 59bce2efadfe Uploaded fubar parents: 9 diff changeset	220 A slight variation taking an input tabular file from which we read the first number as nreps
59bce2efadfe Uploaded fubar parents: 9 diff changeset	221
59bce2efadfe Uploaded fubar parents: 9 diff changeset	222 # note this script takes a single parameter
59bce2efadfe Uploaded fubar parents: 9 diff changeset	223 # number of replicates
59bce2efadfe Uploaded fubar parents: 9 diff changeset	224 ourargs = commandArgs(TRUE)
59bce2efadfe Uploaded fubar parents: 9 diff changeset	225 infname = ourargs[1]
59bce2efadfe Uploaded fubar parents: 9 diff changeset	226 nreps = read.table(infname,head=F)
59bce2efadfe Uploaded fubar parents: 9 diff changeset	227 nreps = unlist(nreps)[1]
59bce2efadfe Uploaded fubar parents: 9 diff changeset	228 nreps = max(c(1,nreps))
59bce2efadfe Uploaded fubar parents: 9 diff changeset	229 nreps = min(c(20,nreps))
59bce2efadfe Uploaded fubar parents: 9 diff changeset	230 print(paste("Using nreps=",nreps))
59bce2efadfe Uploaded fubar parents: 9 diff changeset	231 for (i in 1:nreps) {
59bce2efadfe Uploaded fubar parents: 9 diff changeset	232 foo = runif(100)
59bce2efadfe Uploaded fubar parents: 9 diff changeset	233 bar = rnorm(100)
59bce2efadfe Uploaded fubar parents: 9 diff changeset	234 bar = foo + 0.2*bar
59bce2efadfe Uploaded fubar parents: 9 diff changeset	235 pdf(paste("yet",i,"anotherplot.pdf",sep="_"))
59bce2efadfe Uploaded fubar parents: 9 diff changeset	236 plot(foo,bar,main=paste("Foo by Bar plot ",i),col="maroon", pch=3,cex=0.6)
59bce2efadfe Uploaded fubar parents: 9 diff changeset	237 dev.off()
59bce2efadfe Uploaded fubar parents: 9 diff changeset	238 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
59bce2efadfe Uploaded fubar parents: 9 diff changeset	239 bar = as.matrix(foo)
59bce2efadfe Uploaded fubar parents: 9 diff changeset	240 pdf(paste("yet",i,"anotherheatmap.pdf",sep="_"))
59bce2efadfe Uploaded fubar parents: 9 diff changeset	241 heatmap(bar,main="Random Heatmap")
59bce2efadfe Uploaded fubar parents: 9 diff changeset	242 dev.off()
59bce2efadfe Uploaded fubar parents: 9 diff changeset	243 }
7 1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	244
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	245 A Python example that reverses each row of a tabular file (you'll need to remove the leading spaces
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	246 for this to work if cut and pasted into the script box)::
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	247
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	248 # reverse order of columns in a tabular file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	249 import sys
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	250 inp = sys.argv[1]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	251 outp = sys.argv[2]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	252 i = open(inp,'r')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	253 o = open(outp,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	254 for row in i:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	255 rs = row.rstrip().split('\t')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	256 rs.reverse()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	257 o.write('\t'.join(rs))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	258 o.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	259 i.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	260 o.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	261
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	262 A trivial shell script example to show that it works::
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	263
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	264 #!/bin/bash
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	265 INF=$1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	266 OUTF=$2
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	267 cut -c2,4,6,8,10,12 $INF > $OUTF
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	268
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	269 A trivial perl script example to show that even perl works::
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	270
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	271 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	272 # change all occurances of a string in a file to another string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	273 #
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	274 $oldfile = $ARGV[0];
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	275 $newfile = $ARGV[1];
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	276 $old = "gene";
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	277 $new = "foo";
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	278 open(OF, $oldfile);
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	279 open(NF, ">$newfile");
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	280 # read in each line of the file
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	281 while ($line = <OF>) {
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	282 $line =~ s/$old/$new/;
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	283 print NF $line;
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	284 }
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	285 close(OF);
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	286 close(NF);
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	287
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	288 ]]>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	289
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	290 Citation
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	291
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	292
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	293 Paper_ :
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	294
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	295 Creating re-usable tools from scripts: The Galaxy Tool Factory
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	296 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	297 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	298
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	299
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	300 Licensing
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	301
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	302 Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	303 All rights reserved.
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	304 Licensed under the LGPL_
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	305
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	306 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	307 .. _GTF: https://bitbucket.org/fubar/galaxytoolfactory
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	308 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	309 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	310
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	311
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	312 </help>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	313
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	314 </tool>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	315
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included fubar parents: diff changeset	316

Mercurial > repos > fubar > toolfactory

annotate rgToolFactory.xml @ 24:f87139fe5e09 draft