[Bioperl-pipeline] simplified xml schema with converter supporting.

[Xiao Juguang]

Hi Folks,

I add one xml template called juguang_debut_annotation, which basic do the
same work as genomic_sequence_annotation does, except 2 feature.

1) this schema is intent to support converter, which I will fully implement
soon later. I will give you a detailed introduction when it is done.
2) I simplified the schema to save your typewriting effort. I changed the
Xml2Db.pl to make it recongize both the old and new schema. There are some
examples.Remember this OLD and its following NEW one mean the same thing.

OLD:
    <iohandler id="4">
      <adaptor_id>2</adaptor_id>
      <adaptor_type>DB</adaptor_type>
      <iohandler_type>INPUT</iohandler_type>
      <method>
        <name>fetch_repeatMaskedSeq_by_contig_id</name>
        <rank>1</rank>
        <argument>
          <value>INPUT</value>
          <type>SCALAR</type>
          <rank>1</rank>
        </argument>
      </method>
    </iohandler>

NEW:

 <iohandler id="4" type="INPUT">
  <adaptor id="2" type="DB"/>
  <method name="fetch_repeatMaskedSeq_by_contig_id" rank="1">
   <argument value="INPUT" type="SCALAR" rank="1"/>
  </method>
 </iohandler>

OLD:

    <rule>
      <current_analysis_id>1</current_analysis_id>
      <next_analysis_id>2</next_analysis_id>
      <action>NOTHING</action>
    </rule>
    <rule>
      <current_analysis_id>2</current_analysis_id>
      <next_analysis_id>3</next_analysis_id>
      <action>COPY_ID</action>
    </rule>

NEW:

<rule current="1" next="2" action="NOTHING"/>
 <rule current="2" next="3" action="COPY_ID"/>

I test the new Xml2Db.pl by parse all existing xml under templates
directory, as well as my new xml, juguang_debut_annotation. all tests are
past. And before commit it, I did make test. I do not think this module is
relevant to the core of pipeline..

Through this test, my ConverterAdaptor past the test again.

Need to talk with Shawn and Kiran about furthur simplied scheme. I will find
time to update the dtd later.

Juguang.