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changeset 6:357a3a950661 draft

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Deleted selected files
author kuyt002
date Tue, 24 Jun 2014 07:25:33 -0400
parents bd4013f7e604
children 596a7b43a95b
files .project vennerable/Vennerable.R vennerable/Vennerable.xml vennerable/static/images/Vennerable.R_backup.png vennerable/static/images/Vennerable.xml_backup.png vennerable/tool_dependencies.xml
diffstat 6 files changed, 0 insertions(+), 385 deletions(-) [+]
line wrap: on
line diff
--- a/.project	Tue Jun 24 13:21:35 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>vennerable</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-	</buildSpec>
-	<natures>
-	</natures>
-</projectDescription>
--- a/vennerable/Vennerable.R	Tue Jun 24 13:21:35 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#!/usr/bin/R
-
-# R script to call Vennerable package from galaxy
-# info: alex.bossers@wur.nl
-
-# R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution
-# 1     2       3             4           5       6        7       8         9        10        11
-
-#get cmd line args
-args <- commandArgs()
-	in.file	<- args[6]
-	xData		<- args[7]   # data labels xData of format "a, b, c" and can include spaces
-	weighting	<- args[8] 
-	out.file	<- args[9]
-	plottype	<- args[10]
-	resolution	<- args[11]	#in dpi
-	
-#open lib
-library(Vennerable)
-
-# for labels of bars or bar groups presume column names from data
-if (xData != "default") {
-	# read without header input file (must be tabular)
-	annot_data <- read.table(in.file, header=F, sep="\t")
-	colnames (annot_data) <- strsplit(xData,",")[[1]]
-	Vannot <- Venn(annot_data)
-} else {
-	# read without header input file (must be tabular)
-	annot_data <- read.table(in.file, header=T, sep="\t")
-	Vannot <- Venn(annot_data)
-}
-
-#png(out.file,width = 1600, height = 1600, res = resolution)
-#due to png x11 combination errors its now temporarily a pdf. If not use this line to get a high quality png
-#png(out.file, res = resolution)
-pdf(out.file)
-#svg(out.file)
-# plot it
-if (plottype == "ChowRuskey") {
-	plot(Vannot, type = plottype)
-
-} else if (plottype == "AWFE") {
-	plot(Vannot, doWeights = weighting, type = plottype)
-
-} else if (plottype == "circles") {
-	plot(Vannot)
-
-} else if (plottype == "ellipses"){
-	plot(Vannot, type = "ellipses")
-
-} else if (plottype == "squares"){
-	plot(Vannot, type = "squares")
-
-}
-
-cat ("version 1.0, info: alex.bossers@wur.nl\n")
-dev.off()
-
--- a/vennerable/Vennerable.xml	Tue Jun 24 13:21:35 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-<tool id="Vennerable" name="Vennerable" version="0.9" >
-	<description>: Plot data in Venn or Venn-like diagrams</description>
-	<command>
-	#if $opt.userSpecified == "Yes" 
-		R --slave --vanilla --file=\$VENNERABLE_SCRIPT_PATH/Vennerable.R 
-			--args $inputFile
-			default
-			$weighting
-			$outputFile
-			$plottype
-			$resolution
-			2&gt;$Vennerable_log
-			1&gt;&gt;$Vennerable_log
-	#else
-		R --slave --vanilla --file=\$VENERABLE_SCRIPT_PATH/Vennerable.R
-			--args $inputFile
-			"$opt.xNames" 
-			$weighting
-			$outputFile
-			$plottype
-			$resolution
-			2&gt;$Vennerable_log
-			1&gt;&gt;$Vennerable_log
-	#end if
-	</command>	
-	<inputs>
-		<param name="inputFile" format="tabular" type="data" label="Data set" />
-		<conditional name="opt">
-			<param name="userSpecified" type="select" label="Use column headers as dataset names?">
-				<option value="Yes">Yes</option>
-				<option value="No">No</option>
-			</param>
-			<when value="Yes">
-			</when>
-			<when value="No">
-				<param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/>
-			</when>
-		</conditional>
-		<param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" >
-			<option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted)</option>
-			<option value="ChowRuskey">Chow-Ruskey (always weigthed)</option>
-			<option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option>
-			<option value="circles">Circles (max 3 datasets)</option>
-			<option value="squares">Squares (max 4 datasets non-weighted)</option>
-		</param>
-		<param name="weighting" type="select" label="Use weighting for data in plot" >
-			<option value="FALSE" selected="True">Non-weighted</option>
-			<option value="TRUE">Weighted</option>
-		</param>
-		<param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting. Lower (50) is larger text.&lt;br /&gt;&lt;i&gt;Temporarily it generates a pdf not supporting these functions!&lt;/i&gt;" />
-	</inputs>
-	<outputs>
-<!--		<data name="outputFile" format="png" label="Venn diagram of ${inputFile.name}"/>
--->
-		<data name="outputFile" format="pdf" label="Venn diagram of ${inputFile.name}"/>
-		<data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" />
-	</outputs>
-	<tests>
-		<test>
-		</test>
-	</tests>
-	<requirements>
-		<requirement type="package" version="3.0.3">R_3_0_3</requirement>
-		<requirement type="package" version="3.0">venerable</requirement>
-		<requirement type="set_environment">VENNERABLE_SCRIPT_PATH</requirement>
-	</requirements>
-	<help>
-| 
-
-
-**What it does**
-
-Vennerable V2.0 (09-10-2009)
-
-This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky. 
-
-The tool can take 2 to 7 collumns of data but more are adviced not to be used (for speed and clarity).
-
------
-
-**Input**
-
-It takes a tabular file containing identifiers. Matches will be calculated automatically.
-
-Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded.
-
-::
- 
- DataA	DataB	DataC	DataD
- HUM1	AGK2	AGK2	RTT3
- AGK2	ZZE3	ERT3	ZPD3
- ZPD3	AAW3	RTT3	WER2
- WER2	HUM1	RRW4	DUM1
-
------
-
-**Example**
-
-.. image:: ../static/images/WURtools/VennerablePlot.png 
-
------
-
-**References**
-
-- alex.bossers@wur.nl
-- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ 
-
------
-
-.. class:: infomark
-
-**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-
-
-  </help>
-</tool>
--- a/vennerable/static/images/Vennerable.R_backup.png	Tue Jun 24 13:21:35 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-#!/usr/bin/R
-
-# R script to call Vennerable package from galaxy
-# info: alex.bossers@wur.nl
-
-# R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution
-# 1     2       3             4           5       6        7       8         9        10        11
-
-#get cmd line args
-args <- commandArgs()
-	in.file	<- args[6]
-	xData		<- args[7]   # data labels xData of format "a, b, c" and can include spaces
-	weighting	<- args[8] 
-	out.file	<- args[9]
-	plottype	<- args[10]
-	resolution	<- args[11]	#in dpi
-	
-#open lib
-library(Vennerable)
-
-# for labels of bars or bar groups presume column names from data
-if (xData != "default") {
-	# read without header input file (must be tabular)
-	annot_data <- read.table(in.file, header=F, sep="\t")
-	colnames (annot_data) <- strsplit(xData,",")[[1]]
-	Vannot <- Venn(annot_data)
-} else {
-	# read without header input file (must be tabular)
-	annot_data <- read.table(in.file, header=T, sep="\t")
-	Vannot <- Venn(annot_data)
-}
-
-#png(out.file,width = 1600, height = 1600, res = resolution)
-png(out.file, res = resolution)
-
-# plot it
-if (plottype == "ChowRuskey") {
-	plot(Vannot, type = plottype)
-
-} else if (plottype == "AWFE") {
-	plot(Vannot, doWeights = weighting, type = plottype)
-
-} else if (plottype == "circles") {
-	plot(Vannot)
-
-} else if (plottype == "ellipses"){
-	plot(Vannot, type = "ellipses")
-
-} else if (plottype == "squares"){
-	plot(Vannot, type = "squares")
-
-}
-
-cat ("version 1.0, info: alex.bossers@wur.nl\n")
-dev.off()
-
--- a/vennerable/static/images/Vennerable.xml_backup.png	Tue Jun 24 13:21:35 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,112 +0,0 @@
-<tool id="Vennerable" name="Vennerable" version="0.9" >
-	<description>: Plot data in Venn or Venn-like diagrams</description>
-	<command>
-	#if $opt.userSpecified == "Yes" 
-		R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R 
-			--args $inputFile
-			default
-			$weighting
-			$outputFile
-			$plottype
-			$resolution
-			2&gt;$Vennerable_log
-			1&gt;&gt;$Vennerable_log
-	#else
-		R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/WURtools/R_tools/Vennerable.R
-			--args $inputFile
-			"$opt.xNames" 
-			$weighting
-			$outputFile
-			$plottype
-			$resolution
-			2&gt;$Vennerable_log
-			1&gt;&gt;$Vennerable_log
-	#end if
-	</command>	
-	<inputs>
-		<param name="inputFile" format="tabular" type="data" label="Data set" />
-		<conditional name="opt">
-			<param name="userSpecified" type="select" label="Use column headers as dataset names?">
-				<option value="Yes">Yes</option>
-				<option value="No">No</option>
-			</param>
-			<when value="Yes">
-			</when>
-			<when value="No">
-				<param name="xNames" type="text" label="Alternative data names" value="A,B,C,D" help="(comma-separated)"/>
-			</when>
-		</conditional>
-		<param name="plottype" type="select" label="Plot type to use" help="some other options might get disabled for certain plottypes" >
-			<option value="AWFE" selected="True">AWFE: Edwards-Venn (Non-weighted)</option>
-			<option value="ChowRuskey">Chow-Ruskey (always weigthed)</option>
-			<option value="ellipses">Ellipses (4 datasets only and always non-weighted)</option>
-			<option value="circles">Circles (max 3 datasets)</option>
-			<option value="squares">Squares (max 4 datasets non-weighted)</option>
-		</param>
-		<param name="weighting" type="select" label="Use weighting for data in plot" >
-			<option value="FALSE" selected="True">Non-weighted</option>
-			<option value="TRUE">Weighted</option>
-		</param>
-		<param name="resolution" type="integer" label="Resolution to use (dpi)" value="150" help="Plot features can be sized with this setting. Lower (50) is larger text." />
-	</inputs>
-	<outputs>
-		<data name="outputFile" format="png" label="Venn diagram of ${inputFile.name}"/>
-		<data name="Vennerable_log" format="tabular" label="Vennerable output and error log file" />
-	</outputs>
-	<tests>
-		<test>
-		</test>
-	</tests>
-	<requirements>
-		<requirement type="binary">R</requirement>
-	</requirements>
-	<help>
-| 
-
-
-**What it does**
-
-Vennerable V2.0 (09-10-2009)
-
-This tool will use the Vennerable R package to plot data as weighted or un-weighted diagrams such as Venn, Edwards-Venn and Chow-Rusky. 
-
-The tool can take 2 to 7 collumns of data but more are adviced not to be used (for speed and clarity).
-
------
-
-**Input**
-
-It takes a tabular file containing identifiers. Matches will be calculated automatically.
-
-Be sure to specify headers if you haven't any in your dataset! Otherwise the top row of data will be excluded.
-
-::
- 
- DataA	DataB	DataC	DataD
- HUM1	AGK2	AGK2	RTT3
- AGK2	ZZE3	ERT3	ZPD3
- ZPD3	AAW3	RTT3	WER2
- WER2	HUM1	RRW4	DUM1
-
------
-
-**Example**
-
-.. image:: ../static/images/WURtools/VennerablePlot.png 
-
------
-
-**References**
-
-- alex.bossers@wur.nl
-- Vennerable R package: http://r-forge.r-project.org/projects/vennerable/ 
-
------
-
-.. class:: infomark
-
-**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-
-
-  </help>
-</tool>
--- a/vennerable/tool_dependencies.xml	Tue Jun 24 13:21:35 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<set_environment version="1.0">
-		<environment_variable name="VENNERABLE_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/vennerable/</environment_variable>
-	</set_environment>
-	<package name="R_3_0_2" version="3.0.2">
-        <repository changeset_revision="956709746799" name="package_r_3_0_2" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-                  
-    </package>
-	
-	<package name="venerable" version="3.0">
-         <install version="1.0">
-            <actions>
-                <action type="setup_r_environment">
-                    <repository changeset_revision="956709746799" name="package_r_3_0_2" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="R_3_0_3" version="3.0.3" />
-                    </repository>
-                    <package>http://www.bioconductor.org/packages/devel/bioc/src/contrib/BiocGenerics_0.11.2.tar.gz</package>
-                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/graph_1.42.0.tar.gz</package>
-                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/RBGL_1.40.0.tar.gz</package>
-                    <package>http://cran.r-project.org/src/contrib/RColorBrewer_1.0-5.tar.gz</package>
-                    <package>http://cran.r-project.org/src/contrib/Rcpp_0.11.2.tar.gz</package>
-                    <package>http://cran.r-project.org/src/contrib/plyr_1.8.1.tar.gz</package>
-                    <package>http://cran.r-project.org/src/contrib/reshape_0.8.5.tar.gz</package>
-                    <package>http://cran.r-project.org/src/contrib/gtools_3.4.1.tar.gz</package>                   
-					<package>http://download.r-forge.r-project.org/src/contrib/Vennerable_3.0.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-	</package>
-</tool_dependency>
-