Changeset 1477

Timestamp:

Nov 29, 2011, 2:27:08 PM (12 years ago)

Author:

pawels

Message:

plugin -> plug-in in readme

File:

• extensions/no.uib.ii.magetab/tags/0.9/readme.txt (modified) (9 diffs)

extensions/no.uib.ii.magetab/tags/0.9/readme.txt

@@ -1 @@
-MageTab Exporter Plugin
+MageTab Exporter Plug-in
 ---------------------------
 
-From BASE2 experiment the plugin exports the experimental metadata in MageTab format
+From BASE2 experiment the plug-in exports the experimental metadata in MageTab format
 
 
 I Description
 ----------------
-Executed on an experiment in BASE2, the plugin generates an SDRF and IDF files 
+Executed on an experiment in BASE2, the plug-in generates an SDRF and IDF files 
 (see MageTab specification at http://www.mged.org/mage-tab/) with experiment's metadata, 
 and an archive containing raw data files.
@@ -14 +14 @@
 II Requirements
 ----------------
-The plugin was developed and tested with BASE 2.16.1. BASE 2.17.x versions should also be fine. 
-If you are able to use the plugin with earlier versions of BASE, please let the developer know.
+The plug-in was developed and tested with BASE 2.16.1. BASE 2.17.x versions should also be fine. 
+If you are able to use the plug-in with earlier versions of BASE, please let the developer know.
  
 
@@ -23 +23 @@
   (2) Log in to BASE as a root, browse to Administrate -> Plugins -> Definitions, and click New.
   (3) In the dialog that opens, enter "no.uib.cbu.base.magetabexport.MageTabExporterPlugin" for class,
-    and path to the plugin jar file (e.g. <BASE_HOME>/plugins/MageTabExporter-x.x.jar) for path.
-  (4) In the job agents tab, add job agents that will be able to execute the plugin (if any).
+    and path to the plug-in jar file (e.g. <BASE_HOME>/plugins/MageTabExporter-x.x.jar) for path.
+  (4) In the job agents tab, add job agents that will be able to execute the plug-in (if any).
   (5) Click Save
 
-  The new plugin appears under the name "MageTab exporter" in the plugins list, and is now ready for use.
+  The new plug-in appears under the name "MageTab exporter" in the plug-ins list, and is now ready for use.
   
 
@@ -33 +33 @@
 ----------------
 
-The plugin can be launched from the details page of an experiment. Please make sure that the experiment that is 
+The plug-in can be launched from the details page of an experiment. Please make sure that the experiment that is 
 to be exported is properly created (documented). Use the experiment overview/validation in BASE.
 
-The plugin supports pooled samples, extracts and labeled extracts, but currently the maximum level of 
+The plug-in supports pooled samples, extracts and labeled extracts, but currently the maximum level of 
 nesting of items of one type is 2. This means that pool of samples (and extracts/labeled extracts) is 
 supported, but pool of pooled samples (or extracts/labeled extracts) is not.
 
-The MageTab exporter plugin has following parameters:
+The MageTab exporter plug-in has following parameters:
   - Experiment 
-    the experiment to export, set by default to the one that was open when launching the plugin
+    the experiment to export, set by default to the one that was open when launching the plug-in
   - Save as    
     a path and prefix for the files that are created, e.g. using /home/me/prefix will result
-    in two files being created during the plugin execution: /home/me/prefix_idf.txt and /home/me/prefix_sdrf.txt
+    in two files being created during the plug-in execution: /home/me/prefix_idf.txt and /home/me/prefix_sdrf.txt
   - Save raw data archive as
     name of the zip archive with raw data
@@ -56 +56 @@
     if the content in tab-delimited IDF and SDRF files should be quoted with double quotes
   - Handle missing content by
-    in certain experimental setups missing/empty content is allowed for biosources and/or samples. The plugin 
+    in certain experimental setups missing/empty content is allowed for biosources and/or samples. The plug-in 
     can ignore these missing content and fill empty values with a replacement text (see next parameter). 
-    If you don't expect missing items in your experiment and set the parameter to Error, the plugin will fail 
+    If you don't expect missing items in your experiment and set the parameter to Error, the plug-in will fail 
     with an error message if missing/empty item is found
   - Replace missing content with
@@ -70 +70 @@
     type of annotations holding MGED ontology Material Type terms (see (3) in section V to learn more)
 
-The MageTab exporter plugin supports configuration, so site's default/preferred settings of many parameters can be stored 
+The MageTab exporter plug-in supports configuration, so site's default/preferred settings of many parameters can be stored 
 and reused to ease the execution.  
 
@@ -77 +77 @@
 ----------------
         
-To get most of the plugin capabilities you could:
-  (1) make sure that the format of the author and affiliation fields is parsable by the plugin. 
+To get most of the plug-in capabilities you could:
+  (1) make sure that the format of the author and affiliation fields is parsable by the plug-in. 
   This will allow to split individual authors and automatically map them to institutions they are 
   affiliated with. Format the fields in the following way:
@@ -91 +91 @@
     - line number is the institution mark, e.g institution in line 3 will be mapped to authors with 
       affiliation mark 3.
-    - if you put a number in front of the institution name it will help you check if the plugin did
+    - if you put a number in front of the institution name it will help you check if the plug-in did
       a good job mapping authors with affiliations
     Example: "1 Institute Without a Name, Somestreet 100, 5044 Sometown, Somewhere
@@ -103 +103 @@
   should be enabled for array designs and protocols, and used to set accession ids on the items that 
   had been previously exported to ArrayExpress. If you export an experiment using a design or protocol(s) 
-  with such an annotation, the plugin will pick up identifiers from the annotations, and use them in 
+  with such an annotation, the plug-in will pick up identifiers from the annotations, and use them in 
   the exported SDRF file (Array Ref and Protocol Ref columns). Just remember to set the correct annotation
-  type when you configure the plugin ("ArrayExpress accession AnnotationType" parameter).
+  type when you configure the plug-in ("ArrayExpress accession AnnotationType" parameter).
       
   (3) create an annotation type representing an MGED Ontology term: Material Type. The annotation type 
   should be enabled for biosources, samples, extracts and labeled extracts. If you then annotate your 
-  biomaterials using this annotation type, and select it in the plugin configuration parameter 
-  ("Material Type AnnotationType"), the plugin will use the annotations in the exported SDRF file 
+  biomaterials using this annotation type, and select it in the plug-in configuration parameter 
+  ("Material Type AnnotationType"), the plug-in will use the annotations in the exported SDRF file 
   (Material Type column).
   
-  (4) store some of the settings in a plugin configuration. The annotation types are the best candidates. Also 
+  (4) store some of the settings in a plug-in configuration. The annotation types are the best candidates. Also 
   raw data file types could be predefined in platform specific configurations.