annotate data_manager/data_manager_ceas_fetch_annotations.xml @ 3:df54f8fcc7a7 draft

Version 1.0.2-3: move to conda-based dependency resolution.

<tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
    <requirements>
      <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement>
    </requirements>
    <description>Fetch and install annotation databases for CEAS</description>
    <command interpreter="python">data_manager_ceas_fetch_annotations.py
    "${out_file}"
    "${description}"</command>
    <inputs>
        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
	<param type="text" name="unique_id" label="Internal identifier"
	       help="Identifier string to associate with the annotation e.g. 'mm9_generic'" />
        <param type="text" name="description" value="" size="50"
	       label="Description of annotation"
	       help="Text that will be displayed to the user when selecting which annotation to use" />
        <conditional name="reference_source">
          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
            <option value="web" selected="True">CEAS website</option>
            <option value="server">File on the server</option>
	    <option value="from_wig">Generated from wig file</option>
          </param>
          <when value="web">
            <param type="select" name="annotation_url">
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
	    </param>
          </when>
          <when value="server">
            <param type="text" name="annotation_filename" value="" size="50"
		   label="Full path to CEAS annotation table file on disk" optional="False" />
            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
          </when>
	  <when value="from_wig">
	    <param type="data" format="wig" name="wig_file" value=""
		   label="Wig file to use for the background genome annotation"
		   help="Will be used as input to build_genomeBG" />
	    <param type="select" name="gene_annotation"
		   label="Gene annotation from UCSC">
	      <option value="refGene">refGene</option>
	    </param>
	  </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
	  <!-- No tests defined, yet -->
        </test>
    </tests>
    <help>

.. class:: infomark

**What it does**

Adds a CEAS gene annotation table file to the *ceas_annotations"* data table. The
database file can be downloaded from the CEAS website, imported from a file on the
Galaxy server, or generated from a ``wig`` file in a Galaxy history.

**Notice:** If you leave the identifier or description blank then they will be
generated automatically. 

------

.. class:: infomark

**Fetching, uploading or creating gene annotation table files**

The gene annotation table files are SQLite database files which are on the CEAS website:

 - http://liulab.dfci.harvard.edu/CEAS/usermanual.html

The data manager allows you to fetch a pre-built table from the CEAS website; note
that these are based on the ``RefSeq`` annotation and are only available for a subset
of genome builds.

To create an annotation table for a different genome build or a different annotation,
use the *Generated from wig* file option. This runs the CEAS utility ``build_genomeBG``
to make a custom table from a wig file, which represents the genome background (e.g.
a wig file created from the ``control lambda`` bedgraph file output from MACS2).

Alternatively if you already have an existing custom annotation file then this can be
imported from a path on the Galaxy server.
    </help>
</tool>