--- a/ceas_wrapper.xml	Wed Apr 22 05:34:06 2015 -0400
+++ b/ceas_wrapper.xml	Wed Aug 10 11:04:42 2016 -0400
@@ -1,17 +1,26 @@
-<tool id="ceas" name="CEAS" version="1.0.2-1">
+<tool id="ceas" name="CEAS" version="1.0.2-2">
+  <description>Annotate intervals and scores with genome features</description>
   <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>
+    <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement>
     <requirement type="package" version="3.1.2">R</requirement>
   </requirements>
-  <description>Annotate intervals and scores with genome features</description>
-  <command interpreter="bash">ceas_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output
-  #if (str($wig_file.ext) == 'bigwig')
-    --bigwig $wig_file
-    --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
-  # else
-    --wig $wig_file
+  <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command>
+  <command interpreter="bash">ceas_wrapper.sh
+  $bed_file ${gdb_file.fields.path}
+  $log_output $pdf_report $xls_output
+  #if (str($wig_file) != 'None')
+    #if (str($wig_file.ext) == 'bigwig')
+      --bigwig $wig_file
+      --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
+    #else
+      --wig $wig_file
+    #end if
+  #end if
+  #if (str($extra_bed_file) != 'None')
+    --ebed $extra_bed_file
   #end if
   #if (str($span) and int(str($span)) > 0)
     --span $span
@@ -22,28 +31,73 @@
   --rel-dist $relative_distance</command>
   <inputs>
     <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
-    <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" />
+    <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"
+	   help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
     <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
     <param name="gdb_file" type="select" label="Gene annotation table">
       <options from_data_table="ceas_annotations">
-	<filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="0" />
-        <validator type="no_options" message="No tables are available for the selected input"/>
       </options>
+      <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" />
+      <validator type="no_options" message="No tables are available for the selected input"/>
     </param>
-    <param name="span" type="integer" label="Span from TSS and TTS in the gene-centered annotation (bp)" help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions" value="3000" />
-    <param name="sizes_lower" type="integer" label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)" value="1000" />
-    <param name="sizes_middle" type="integer" label="Middle interval for promoter/downstream sizes (bp)" value="2000" help="Values > 10000bp are automatically fixed to 10000bp" />
-    <param name="sizes_upper" type="integer" label="Upper interval for promoter/downstream sizes (bp)" value="3000" help="Values > 10000bp are automatically fixed to 10000bp" />
-    <param name="bisizes_lower" type="integer" label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500" />
-    <param name="bisizes_upper" type="integer" label="Upper interval for bidirectional-promoter sizes (bp)" value="5000" help="Values > 20000bp are automatically fixed to 20000bp" />
-    <param name="profiling_resolution" type="integer" label="Wig profiling resolution (bp)" value="50" help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error" />
-    <param name="relative_distance" type="integer" label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000" />
+    <param name="span" type="integer"
+	   label="Span from TSS and TTS in the gene-centered annotation (bp)"
+	   help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions (--span)" value="3000" />
+    <param name="sizes_lower" type="integer"
+	   label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)"
+	   value="1000" help=" (--sizes)" />
+    <param name="sizes_middle" type="integer"
+	   label="Middle interval for promoter/downstream sizes (bp)" value="2000"
+	   help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
+    <param name="sizes_upper" type="integer"
+	   label="Upper interval for promoter/downstream sizes (bp)" value="3000"
+	   help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
+    <param name="bisizes_lower" type="integer"
+	   label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500"
+	   help="(--bisizes)" />
+    <param name="bisizes_upper" type="integer"
+	   label="Upper interval for bidirectional-promoter sizes (bp)" value="5000"
+	   help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" />
+    <param name="profiling_resolution" type="integer"
+	   label="Wig profiling resolution (bp)" value="50"
+	   help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error (--pf-res)" />
+    <param name="relative_distance" type="integer"
+	   label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000"
+	   help="(--rel-dist)" />
   </inputs>
   <outputs>
     <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
     <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
     <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
   </outputs>
+  <tests>
+    <test>
+      <!-- Test with bed input only -->
+      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
+      <param name="gdb_file" value="galGal3_test" />
+      <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/>
+      <output name="pdf_report" file="ceas_out1.pdf" />
+      <output name="xls_output" file="ceas_out1.xls" />
+    </test>
+    <test>
+      <!-- Test with bed & very small wig input -->
+      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
+      <param name="wig_file" value="ceas_in.wig" ftype="wig" />
+      <param name="gdb_file" value="galGal3_test" />
+      <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/>
+      <output name="pdf_report" file="ceas_out2.pdf" />
+      <output name="xls_output" file="ceas_out2.xls" />
+    </test>
+    <test>
+      <!-- Test with bed & bigwig input -->
+      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
+      <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" />
+      <param name="gdb_file" value="galGal3_test" />
+      <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/>
+      <output name="pdf_report" file="ceas_out3.pdf" />
+      <output name="xls_output" file="ceas_out3.xls" />
+    </test>
+  </tests>
   <help>
 **What it does**
 
@@ -57,6 +111,30 @@
 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
 which might be too subtle to detect from ChIP peaks alone.
 
+**Usage**
+
+CEAS takes the following inputs:
+
+ * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS
+   peak caller)
+ * WIG or bigWIG file with a continuous ChIP enrichment signal
+ * Gene annotation table (provided as reference data)
+
+Optionally it can also take a BED file describing extra regions of interest (for example
+non-coding regions).
+
+The analysis modules are:
+
+ * **ChIP region annotation:** estimates the relative enrichment level of ChIP regions in
+   each gene feature with respect to the whole genome.
+ * **Gene-centered annotation:** identifies genes associated with ChIP regions to infer
+   the direct regulatory gene targets of the binding factor of interest.
+ * **Average signal profiling within/near important genomic features:** displays continuous
+   ChIP enrichment signal within/around important gene features to help visualize the
+   average binding patterns.
+
+**Background**
+
 This tool is compatible with the ceasBW version of CEAS from the Cistrome package
 obtained from
 
@@ -71,4 +149,12 @@
 
 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
   </help>
+  <citations>
+    <!--
+    See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+    Can be either DOI or Bibtex
+    Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
+    -->
+    <citation type="doi">10.1093/bioinformatics/btp479</citation>
+  </citations>
 </tool>