Changeset 1476


Ignore:
Timestamp:
Nov 29, 2011, 2:26:54 PM (10 years ago)
Author:
pawels
Message:

plugin -> plug-in in readme

File:
1 edited

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  • extensions/no.uib.ii.magetab/trunk/readme.txt

    r1474 r1476  
    1 MageTab Exporter Plugin
     1MageTab Exporter Plug-in
    22---------------------------
    33
    4 From BASE2 experiment the plugin exports the experimental metadata in MageTab format
     4From BASE2 experiment the plug-in exports the experimental metadata in MageTab format
    55
    66
    77I Description
    88----------------
    9 Executed on an experiment in BASE2, the plugin generates an SDRF and IDF files
     9Executed on an experiment in BASE2, the plug-in generates an SDRF and IDF files
    1010(see MageTab specification at http://www.mged.org/mage-tab/) with experiment's metadata,
    1111and an archive containing raw data files.
     
    1414II Requirements
    1515----------------
    16 The plugin was developed and tested with BASE 2.16.1. BASE 2.17.x versions should also be fine.
    17 If you are able to use the plugin with earlier versions of BASE, please let the developer know.
     16The plug-in was developed and tested with BASE 2.16.1. BASE 2.17.x versions should also be fine.
     17If you are able to use the plug-in with earlier versions of BASE, please let the developer know.
    1818 
    1919
     
    2323  (2) Log in to BASE as a root, browse to Administrate -> Plugins -> Definitions, and click New.
    2424  (3) In the dialog that opens, enter "no.uib.cbu.base.magetabexport.MageTabExporterPlugin" for class,
    25     and path to the plugin jar file (e.g. <BASE_HOME>/plugins/MageTabExporter-x.x.jar) for path.
    26   (4) In the job agents tab, add job agents that will be able to execute the plugin (if any).
     25    and path to the plug-in jar file (e.g. <BASE_HOME>/plugins/MageTabExporter-x.x.jar) for path.
     26  (4) In the job agents tab, add job agents that will be able to execute the plug-in (if any).
    2727  (5) Click Save
    2828
    29   The new plugin appears under the name "MageTab exporter" in the plugins list, and is now ready for use.
     29  The new plug-in appears under the name "MageTab exporter" in the plug-ins list, and is now ready for use.
    3030 
    3131
     
    3333----------------
    3434
    35 The plugin can be launched from the details page of an experiment. Please make sure that the experiment that is
     35The plug-in can be launched from the details page of an experiment. Please make sure that the experiment that is
    3636to be exported is properly created (documented). Use the experiment overview/validation in BASE.
    3737
    38 The plugin supports pooled samples, extracts and labeled extracts, but currently the maximum level of
     38The plug-in supports pooled samples, extracts and labeled extracts, but currently the maximum level of
    3939nesting of items of one type is 2. This means that pool of samples (and extracts/labeled extracts) is
    4040supported, but pool of pooled samples (or extracts/labeled extracts) is not.
    4141
    42 The MageTab exporter plugin has following parameters:
     42The MageTab exporter plug-in has following parameters:
    4343  - Experiment
    44     the experiment to export, set by default to the one that was open when launching the plugin
     44    the experiment to export, set by default to the one that was open when launching the plug-in
    4545  - Save as   
    4646    a path and prefix for the files that are created, e.g. using /home/me/prefix will result
    47     in two files being created during the plugin execution: /home/me/prefix_idf.txt and /home/me/prefix_sdrf.txt
     47    in two files being created during the plug-in execution: /home/me/prefix_idf.txt and /home/me/prefix_sdrf.txt
    4848  - Save raw data archive as
    4949    name of the zip archive with raw data
     
    5656    if the content in tab-delimited IDF and SDRF files should be quoted with double quotes
    5757  - Handle missing content by
    58     in certain experimental setups missing/empty content is allowed for biosources and/or samples. The plugin
     58    in certain experimental setups missing/empty content is allowed for biosources and/or samples. The plug-in
    5959    can ignore these missing content and fill empty values with a replacement text (see next parameter).
    60     If you don't expect missing items in your experiment and set the parameter to Error, the plugin will fail
     60    If you don't expect missing items in your experiment and set the parameter to Error, the plug-in will fail
    6161    with an error message if missing/empty item is found
    6262  - Replace missing content with
     
    7070    type of annotations holding MGED ontology Material Type terms (see (3) in section V to learn more)
    7171
    72 The MageTab exporter plugin supports configuration, so site's default/preferred settings of many parameters can be stored
     72The MageTab exporter plug-in supports configuration, so site's default/preferred settings of many parameters can be stored
    7373and reused to ease the execution. 
    7474
     
    7777----------------
    7878       
    79 To get most of the plugin capabilities you could:
    80   (1) make sure that the format of the author and affiliation fields is parsable by the plugin.
     79To get most of the plug-in capabilities you could:
     80  (1) make sure that the format of the author and affiliation fields is parsable by the plug-in.
    8181  This will allow to split individual authors and automatically map them to institutions they are
    8282  affiliated with. Format the fields in the following way:
     
    9191    - line number is the institution mark, e.g institution in line 3 will be mapped to authors with
    9292      affiliation mark 3.
    93     - if you put a number in front of the institution name it will help you check if the plugin did
     93    - if you put a number in front of the institution name it will help you check if the plug-in did
    9494      a good job mapping authors with affiliations
    9595    Example: "1 Institute Without a Name, Somestreet 100, 5044 Sometown, Somewhere
     
    103103  should be enabled for array designs and protocols, and used to set accession ids on the items that
    104104  had been previously exported to ArrayExpress. If you export an experiment using a design or protocol(s)
    105   with such an annotation, the plugin will pick up identifiers from the annotations, and use them in
     105  with such an annotation, the plug-in will pick up identifiers from the annotations, and use them in
    106106  the exported SDRF file (Array Ref and Protocol Ref columns). Just remember to set the correct annotation
    107   type when you configure the plugin ("ArrayExpress accession AnnotationType" parameter).
     107  type when you configure the plug-in ("ArrayExpress accession AnnotationType" parameter).
    108108     
    109109  (3) create an annotation type representing an MGED Ontology term: Material Type. The annotation type
    110110  should be enabled for biosources, samples, extracts and labeled extracts. If you then annotate your
    111   biomaterials using this annotation type, and select it in the plugin configuration parameter
    112   ("Material Type AnnotationType"), the plugin will use the annotations in the exported SDRF file
     111  biomaterials using this annotation type, and select it in the plug-in configuration parameter
     112  ("Material Type AnnotationType"), the plug-in will use the annotations in the exported SDRF file
    113113  (Material Type column).
    114114 
    115   (4) store some of the settings in a plugin configuration. The annotation types are the best candidates. Also
     115  (4) store some of the settings in a plug-in configuration. The annotation types are the best candidates. Also
    116116  raw data file types could be predefined in platform specific configurations.
    117117 
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