comparison macros.xml @ 1:6d44e7f6513f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde

0:dca536c5cca5

    <param name="w_beta" label="Tail mass at which window length is determined"
        help="(--w_beta)" optional="True" type="float"/>
    <param name="w_length" label="Window Length"
        help="(--w_length)" optional="True" type="integer" />
  </xml>
  <xml name="input_hmm">
    <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
  </xml>
  <xml name="input_msa">
    <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"

**Advanced Documentation**

A more detailed look at the internals of the various filter pipelines was
posted on the `developer's blog <http://selab.janelia.org/people/eddys/blog/?p=508>`__.
The information posted there may be useful to those who are struggling with
poor-scoring sequences.

]]></token>
  <token name="@ADV_OPTS_HELP@"><![CDATA[

  <token name="@ATTRIBUTION@"><![CDATA[

Attribution
-----------

This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/
Internally the software is cited as:

::

    # hmmscan :: search sequence(s) against a profile database

The wrappers were written by Eric Rasche and is licensed under Apache2_. The
documentation is copied from the HMMER3 documentation.

.. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
.. _HMMER3: http://hmmer.janelia.org/


  ]]></token>
  <token name="@HELP_PRE@"><![CDATA[

1:6d44e7f6513f

    <param name="w_beta" label="Tail mass at which window length is determined"
        help="(--w_beta)" optional="True" type="float"/>
    <param name="w_length" label="Window Length"
        help="(--w_length)" optional="True" type="integer" />
  </xml>
  <token name="@INPUTHMMCHOICE@">
#if $input_hmm_conditional.input_hmm_source == "history":
    '$input_hmm_conditional.hmmfile'
#else:
    '$input_hmm_conditional.index.fields.db_path'
#end if
  </token>
  <xml name="input_hmm_choice">
    <conditional name="input_hmm_conditional">
      <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" >
        <option value="indexed" selected="True">Use a built-in HMM model database</option>
        <option value="history">Use a HMM database from history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator">
          <options from_data_table="hmm_database">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
          </options>
        </param>
      </when>
      <when value="history">
        <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
      </when>  <!-- history -->
    </conditional>  <!-- input_hmm_conditional -->
  </xml>
  <xml name="input_hmm">
    <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
  </xml>
  <xml name="input_msa">
    <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"

**Advanced Documentation**

A more detailed look at the internals of the various filter pipelines was
posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__.
The information posted there may be useful to those who are struggling with
poor-scoring sequences.

]]></token>
  <token name="@ADV_OPTS_HELP@"><![CDATA[

  <token name="@ATTRIBUTION@"><![CDATA[

Attribution
-----------

This Galaxy tool relies on HMMER3_
Internally the software is cited as:

::

    # hmmscan :: search sequence(s) against a profile database

The wrappers were written by Eric Rasche and is licensed under Apache2_. The
documentation is copied from the HMMER3 documentation.

.. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
.. _HMMER3: http://hmmer.org/


  ]]></token>
  <token name="@HELP_PRE@"><![CDATA[