Changeset 776 for plugins/base1/se.lu.onk.MergeBioAssay

Timestamp:

Sep 18, 2008, 7:21:18 PM (15 years ago)

Author:

Jari Häkkinen

Message:

Addresses #137.

Location:

plugins/base1/se.lu.onk.MergeBioAssay

Files:

• . (added)
• tags (added)
• trunk (moved) (moved from plugins/base1/se.lu.onk/trunk/MergeBioAssay)
• trunk/README (copied) (copied from plugins/base1/se.lu.onk.ReplicateError/trunk/README) (10 diffs)
• trunk/build.xml (copied) (copied from plugins/base1/se.lu.onk.ReplicateError/trunk/build.xml) (6 diffs)
• trunk/doc/mergebioassay.base (modified) (1 diff)
• trunk/doc/run (modified) (1 diff)
• trunk/license.txt (copied) (copied from plugins/base1/se.lu.onk.ReplicateError/trunk/license.txt)

plugins/base1/se.lu.onk.MergeBioAssay/trunk/README

@@ -1 +1 @@
 $Id$
 
-= About `se.lu.onk.ReplicateError` =
+= About `se.lu.onk.MergeBioAssay` =
 
-The `se.lu.onk.ReplicateError` plug-in for BASE is 
+The `se.lu.onk.MergeBioAssay` plug-in for BASE is 
 
-`se.lu.onk.ReplicateError` is free software. See the file license.txt for
+`se.lu.onk.MergeBioAssay` is free software. See the file license.txt for
 copying conditions.
 
@@ -14 +14 @@
 == Downloading ==
 
-`se.lu.onk.ReplicateError` can be obtained from
+`se.lu.onk.MergeBioAssay` can be obtained from
 
   http://baseplugins.thep.lu.se/wiki/PluginDownload
@@ -26 +26 @@
 http://baseplugins.thep.lu.se. These installation instructions only
 describe how to get the plug-in to work with the Base1PluginExecuter
-in the latest BASE version 2. BASE 1.2 installers should enable one
-line in files AAtabs.html and WAtabs.html, read the information in
-these short files.''
+in the latest BASE version 2.''
 
 If you downloaded a binary package you only need to follow these
@@ -42 +40 @@
 {{{
   # cd /path/to/base/plugins
-  # download ReplicateError-version.tgz
-  # untar ReplicateError-version.tgz
-  # ln -s ReplicateError-version ReplicateError
+  # download MergeBioAssay-version.tgz
+  # untar MergeBioAssay-version.tgz
+  # ln -s MergeBioAssay-version MergeBioAssay
 }}}
-The symbolical link in the last line above allows for easier change to
+The symbolic link in the last line above allows for easier change to
 future version of the plug-in.
 {{{
   # Log in to your BASE as admin
-  # Upload the configuration files `pluginConfigurationAA.base` and
-    `pluginConfigurationWA.base`.
-  # Create/update one configuration each for across and within assays
-    mode of the ReplciateError plug-in where you select the plug-in
-    defintion files `pluginConfigurationAA.base` and
-    `pluginConfigurationWA.base`, respectively. BASE will respond that
-    plug-ins where configured but ...
-  # Re-configure the plug-ins without selecting a file, set the
-    `Plugin executables path` and proceed to next window by clicking
+  # Upload the configuration file `mergebioassay.base`
+  # Create/update a configuration for the plug-in where you select the
+    plug-in defintion files `mergebioassay.base`. BASE will respond
+    that plug-ins where configured but ...
+  # Re-configure the plug-in without selecting a file, set the `Plugin
+    executables path` and proceed to next window by clicking
     `Next`. This is explained in the BASE documentation and needs to
     be done even when you update your plug-in.
   # In this parameter window set the `Name of executable`. The value
     of this parameter and `Plugin executables path` should add up to
-    the absolute path to the binaries `runAA` and `runWA`, i.e.,
-    /path/to/base/plugins/ReplicateError/runAA. How this string looks
+    the absolute path to the binary `run`, i.e.,
+    /path/to/base/plugins/MergeBioAssay/run. How this string looks
     like depends on your plug-in directory structure.
   # Test the plug-ins and when you are satisfied, share it to your
@@ -73 +68 @@
 == Compiling ==
 
-You must checkout the `se.lu.onk.ReplicateError` from the repository,
+You must checkout the `se.lu.onk.MergeBioAssay` from the repository,
 follow the instructions below. Then download and untar the
 `se.lu.onk.BaseFile` package available from
@@ -80 +75 @@
 {{{
   check out project, see instructions below
-  # cd /path/to/se.lu.onk.ReplicateError
+  # cd /path/to/se.lu.onk.MergeBioAssay
   # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz
   # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz.MD5
@@ -91 +86 @@
 It is important that the `BaseFile` package is located in directory
 `BaseFile`. Now simple issue `ant`. This will create a jar file
-`dist/ReplicateError.jar`.
+`dist/MergeBioAssay.jar`.
 
 
 == Creating a distribution ==
 
-Update the version number (make sure they match) in `build.xml`,
-`lib/pluginConfigurationAA.base`, and `lib/pluginConfigurationWA.base`.
-Issue `ant package`. This creates a distribution package with all
-required components, including BaseFile.jar and associated files.
+Update the version number in `build.xml`, and issue `ant
+package`. This creates a distribution package with all required
+components, including BaseFile.jar and associated files.
 
 
 == Bug Reporting ==
 
-You can report `se.lu.onk.ReplicateError` bugs on 
+You can report `se.lu.onk.MergeBioAssay` bugs on 
 
   http://baseplugins.thep.lu.se/newticket
@@ -113 +107 @@
 == Subversion Access ==
 
-The `se.lu.onk.ReplicateError` source repository is available via anonymous
+The `se.lu.onk.MergeBioAssay` source repository is available via anonymous
 subversion access, issue:
 
-  `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.ReplicateError/trunk se.lu.onk.ReplicateError`
+  `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.MergeBioAssay/trunk se.lu.onk.MergeBioAssay`
 
 There is no guarantees about the contents or quality of the latest
@@ -122 +116 @@
 is known to be broken to be committed to the repository. Use at your
 own risk. You may prefer to check out a released version instead, then
-replace `trunk` with `tags/release-number` in the above example.
+replace `trunk` with `tags/version` in the above example.
 
 
@@ -130 +124 @@
 Copyright (C) 2008 Jari Häkkinen
 
-This file is part of the se.lu.onk.ReplicateError plug-in for
+This file is part of the se.lu.onk.MergeBioAssay plug-in for
 BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is
 http://base.thep.lu.se

plugins/base1/se.lu.onk.MergeBioAssay/trunk/build.xml

@@ -6 +6 @@
     Copyright (C) 2008 Jari Hakkinen
 
-    This file is part of the se.lu.onk.ReplicateError plug-in for
+    This file is part of the se.lu.onk.MergeBioAssay plug-in for
     BASE. Available at http://baseplugins.thep.lu.se/ and BASE web
     site is http://base.thep.lu.se
@@ -23 +23 @@
     along with BASE. If not, see <http://www.gnu.org/licenses/>.
 -->
-<project name="se.lu.onk.ReplicateError plug-in for BASE"
+<project name="se.lu.onk.MergeBioAssay plug-in for BASE"
          default="dist" basedir=".">
   <description>
-    This build file is used for se.lu.onk.ReplicateError plug-in for
+    This build file is used for se.lu.onk.MergeBioAssay plug-in for
     BASE created at the Department of Oncology, Lund University,
     Sweden.
@@ -40 +40 @@
        1.0, 1.1, 1.2pre
     -->
-  <property name="version" value="1.3pre" />
+  <property name="version" value="2.1pre" />
 
   <property name="basefilejar" value="BaseFile" />
   <property name="build" location="build" />
   <property name="dist" location="dist" />
-  <property name="lib" location="lib" />
-  <property name="package" value="replicateerror"/>
-  <property name="packagestring" value="ReplicateError-${version}" />
+  <property name="doc" location="doc" />
+  <property name="package" value="mergebioassay"/>
+  <property name="packagestring" value="MergeBioAssay-${version}" />
   <property name="src" location="src" />
   
@@ -87 +87 @@
   <target name="dist" depends="compile">
     <mkdir dir="${dist}" />
-    <jar destfile="${dist}/ReplicateError.jar">
+    <jar destfile="${dist}/MergeBioAssay.jar">
       <fileset dir="${build}" />
       <manifest>
         <attribute name="Built-By" value="${user.name}"/>
-        <attribute name="Main-Class" value="replicateerror.ReplicateError"/>
+        <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/>
       </manifest>
     </jar>
@@ -104 +104 @@
     <mkdir dir="${package}/${basefilejar}"/>
     <copy todir="${package}">
-      <fileset file="${dist}/ReplicateError.jar" />
-      <fileset dir="${lib}" />
+      <fileset file="${dist}/MergeBioAssay.jar" />
+      <fileset dir="${doc}" />
       <fileset file="license.txt" />
       <fileset file="README" />
@@ -112 +112 @@
       <fileset dir="${basefilejar}" />
     </copy>
-    <replace file="${package}/pluginConfigurationAA.base">
-      <replacefilter 
-        token="@VERSION@"
-        value="${version}"
-      />
-    </replace>
-    <replace file="${package}/pluginConfigurationWA.base">
+    <replace dir="${package}">
+      <include name="*.base" />
       <replacefilter 
         token="@VERSION@"

plugins/base1/se.lu.onk.MergeBioAssay/trunk/doc/mergebioassay.base

@@ -2 +2 @@
 section plugin
 uniqueName  onk.lu.se/johan_enell/merge_bioassays
-versionNumber 2.0
+versionNumber @VERSION@
 name  Transformation: Merge bioassays
 descr Using this plugin base-users can merge together bioassays by grouping them according to annotation types or syntactical differences in the name. There are four different method for calculating the new values. They differ in what kind of mean they are using (arithmetic or geometric) and if they are merging on ratio or intensity. \r\n\r\nFor each group the parents are saved so the link to the raw data is preserved. Annotations for the bioassays are saved if sample1 is the same for each assay in each group.\r\n\r\nIMPORTANT\r\nIf you have merged assays in a group, BASE 1.2.10 will have difficulties to export data Merged on reporter from the parents RawBioAssays. If you for instance export '[Raw] Spot diameter' for a merged assay, each reporter might be associated with values from several RawBioAssays but only one such value will be exported. This is a known limitation of base 1.2.10 and will be fix in future versions. \r\n\r\nMerge methods\r\n\r\nGeometric mean of ratio:\r\n  This method calculates the geometric mean of the ratios in each group per position.\r\n\r\nArithmetic mean of ratio:\r\n  This method calculates the arithmetic mean of the ratios in each group per position.\r\n\r\nArithmetic mean of intensity:\r\n  This method calculates the arithmetic mean of the intensities in each group per position.\r\n\r\nRatio of ratio:\r\n  This method works a little bit different from the others. It demands that each group consists of exactly two bioassays. Then it will create a new ratio for each spot with one of the assays over the other, depending on what the user has specified in the ratio parameters. \r\n\r\nPARAMETERS:\r\nAssayname\r\nGroup\r\nNew name\r\nMerge method\r\nRatio\r\n\r\n\r\nAssayname - This parameter specifies how the name of the assays is constructed. Use  %0-%9 as wildcards and then put any character(s) between as delimiters. For example assay name Assay_1_A can be divided into three parts. By setting the parameter to %1_%2_%3 the plugin will read assay name assay_1_A and set %1=Assay, %2=1 and %3=A. Thus, if your assays have names constructed in the same way merge can sort the assays in groups depending on %1, %2 or %3.\r\n\r\nGroup - This will specify how the assays will be grouped together. It can either be a %-number used in assayname or an annotation type.\r\n\r\nExample1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.\r\n \r\n 1a: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %2 will sort the assays into two groups.\r\n\r\n One group were %2=1 (assays Assay_1_A and Assay_1_B)\r\n One group were %2=2  (assays Assay_2_A and Assay_2_B) \r\n\r\n 1b: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %3 will sort the assays into two groups.\r\n\r\n One group were %3=A (assays Assay_1_A and Assay_2_A)\r\n One group were %3=B  (assays Assay_1_B and Assay_1_B) \r\n\r\nNew name - This text will be used in the name of the new merged assays. The name will be this string followed by the groupname.\r\n\r\nMerge method - Choose one of the methodes described above.\r\n\r\nRatio - If merge method "ratio of ratio" is chosen the form of the ratio must be specified. This is done either in the ratio parameter or in ratio annotation type and ratio annotation value. In the ratio parameter you can choose a  %-number followed by the two values it can take. The last character in the string must be the delimiter the user has choosen ot use. The other way a user can specify the ratio is by choosing an annotation type in the list and specify the values in the annotation values parameter. This is done by writing the values with the delimiter used last. \r\n\r\nex.\r\n\r\n%1|vr1|vr2|\r\n\r\nThis will take the values from %1 in the assayname and put the assay with value vr1 over the assay with values vr2. Notice that the final character is the delimiter (this can of course be any character).\r\n\r\nExample2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.\r\n\r\n 1a: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222  = %2 will sort the assays into two groups.\r\n\r\n One group were %2=1 (assays Assay_1_A and Assay_1_B)\r\n One group were %2=2  (assays Assay_2_A and Assay_2_B)\r\n\r\nBy setting parameter \221Ratio\222 = %3|A|B| ratios of ratios will be created as:\r\n        Assay_1_A / Assay_1_B\r\n        Assay_2_A / Assay_2_B\r\n \r\nArithmetic mean\r\nhttp://mathworld.wolfram.com/ArithmeticMean.html\r\nGeometric mean\r\nhttp://mathworld.wolfram.com/GeometricMean.html\r\n

plugins/base1/se.lu.onk.MergeBioAssay/trunk/doc/run

@@ -2 +2 @@
 
 progdir="`dirname \"$0\"`"
-java -cp "$CLASSPATH:$progdir/mergebioassay.jar" mergebioassay/MergeBioAssay stdin.txt
+java -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/mergebioassay.jar" mergebioassay/MergeBioAssay stdin.txt