Specify the location of the BED files available for filtering

mutspecFilter.xml

@@ -47,10 +47,10 @@
     <param name="segDup" type="boolean" checked="true" truevalue="--segDup" falsevalue="" label="Filter against SegDup database" help="Remove variants present at &#62;= 0.9 frequency in the genomic duplicate segments database" />
     <param name="esp" type="boolean" checked="true" truevalue="--esp" falsevalue="" label="Filter against the ESP database" help="Remove variants present at frequency &#62; 0.001 in the Exome Sequencing Project database (only valid for human genomes)" />
     <param name="thG" type="boolean" checked="true" truevalue="--thG" falsevalue="" label="Filter against the 1000g database project" help="Remove variants present at frequency &#62; 0.001 in the 1000 genome database (only valid for human genomes)" />
-    <param name="exac" type="boolean" checked="true" truevalue="--exac" falsevalue="" label="Filter against the ExAC database" help="Remove variants present at frequency &#62; 0.001 in the EXome Agregate Consortium database" />
+    <param name="exac" type="boolean" checked="true" truevalue="--exac" falsevalue="" label="Filter against the ExAC database" help="Remove variants present at frequency &#62; 0.001 in the EXome Agregate Consortium database (only valid for human genomes)" />
 
     <repeat name="filters" title="Additional filters">
-    	<param name="reference" type="data" format="bed" label="bed file reference" help="filter regions"/>
+    	<param name="reference" type="data" format="bed" label="Reference file (bed or vcf)" help="Remove variants present in the reference file"/>
     </repeat>
 
 </inputs>
@@ -63,11 +63,11 @@
 
 **What it does**
 
-Filter a file annotated with MutSpec-Annot tool. Variants present in public databases (dbSNP, SegDup, ESP, 1000 genome obtained from Annovar) will be removed from the input file (with frequency limits described above).
+Filter a file annotated with MutSpec-Annot tool. Variants present in public databases obtained from Annovar will be removed from the input file (with frequency limits described above).
 
 .. class:: warningmark
 
-The databases ESP and 1000 genome can be used only for human genomes
+The databases ESP, 1000 genome and ExAC can be used only for human genomes
 
 --------------------------------------------------------------------------------------------------------------------------------------------------
 
@@ -86,6 +86,13 @@ Tab delimited text files generated by MutSpec-Annot tool.
 You eventually would like to filter for additional features like repeats and tandem repeats.
 You just need to provide the reference in vcf or bed format.
 
+.. class:: infomark
+
+Reference files are available on IARC Galaxy Shared Data.
+On the top panel click on "Shared Data" and select "Data Libraries".
+The category "BED annotations" contains reference files for different genomes.
+
+
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 **Output**