add gff selectors to cached

tools/featurecounts/featurecounts.xml

@@ -49,7 +49,7 @@
             $read_filtering_parameters.primary
             $read_filtering_parameters.ignore_dup
 
-            #if $anno.anno_select=="history":
+            #if $anno.anno_select!="builtin":
                 -t '$anno.gff_feature_type'
                 -g '$anno.gff_feature_attribute'
                     $anno.summarization_level
@@ -177,6 +177,27 @@
                     </options>
                     <validator type="no_options" message="A cached annotation file is not available for the genome build associated with the selected input file"/>
                 </param>
+                <param name="gff_feature_type"
+                    type="text"
+                    value="exon"
+                    argument="-t"
+                    label="GFF feature type filter"
+                    help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/>
+
+                <param name="gff_feature_attribute"
+                    type="text"
+                    value="gene_id"
+                    argument="-g"
+                    label="GFF gene identifier"
+                    help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization. Ex: if the 9th column is 'gene_id &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
+
+                <param name="summarization_level"
+                    type="boolean"
+                    truevalue=" -f"
+                    falsevalue=""
+                    argument="-f"
+                    label="On feature level"
+                    help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level."/>
             </when>
             <when value="history">
                 <param name="reference_gene_sets"