--- a/data_manager/data_manager_ceas_fetch_annotations.xml	Wed Apr 22 05:34:06 2015 -0400
+++ b/data_manager/data_manager_ceas_fetch_annotations.xml	Wed Aug 10 11:04:42 2016 -0400
@@ -1,23 +1,27 @@
 <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
+    <requirements>
+      <requirement type="package" version="1.2.5">python_mysqldb</requirement>
+      <requirement type="package" version="0.7.1">bx_python</requirement>
+      <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
+    </requirements>
     <description>Fetch and install annotation databases for CEAS</description>
     <command interpreter="python">data_manager_ceas_fetch_annotations.py
-    #if str( $reference_source.reference_source_selector ) == "ceas_web"
-      --download=$reference_source.annotation_url
-    #end if
     "${out_file}"
     "${description}"</command>
     <inputs>
         <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
-        <param type="text" name="description" value="" label="Description of annotation" />
+	<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="ceas_web" selected="True">CEAS website</option>
-	    <!-- Not implemented for now
-            <option value="history">History</option>
-	    -->
-            <option value="directory">Directory on Server</option>
+            <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="ceas_web">
+          <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>
@@ -29,15 +33,20 @@
 	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
 	    </param>
           </when>
-	  <!-- Not implemented for now
-          <when value="history">
-            <param name="input_annotation" type="data" format="fasta" label="Annotation File" multiple="False" optional="False" />
-          </when>
-	  -->
-          <when value="directory">
-            <param type="text" name="annotation_filename" value="" label="Full path to CEAS annotation table file on disk" optional="False" />
+          <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>
@@ -45,29 +54,42 @@
     </outputs>
     <tests>
         <test>
-            <param name="dbkey" value="anoGam1"/>
-            <param name="sequence_name" value=""/>
-            <param name="sequence_desc" value=""/>
-            <param name="sequence_id" value=""/>
-            <param name="reference_source_selector" value="history"/>
-            <param name="input_fasta" value="phiX174.fasta"/>
-            <param name="sort_selector" value="as_is"/>
-            <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
+	  <!-- No tests defined, yet -->
         </test>
     </tests>
     <help>
+
+.. class:: infomark
+
 **What it does**
 
-Fetches an annotation database from the CEAS website, Galaxy history, or a server directory
-and populates the "ceas_annotations" data table.
+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
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+**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>