--- a/freebayes.xml	Thu May 04 11:34:13 2017 -0400
+++ b/freebayes.xml	Tue Jun 06 11:44:38 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-3">
+<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">
     <description>bayesian genetic variant detector</description>
     <macros>
         <import>macros.xml</import>
@@ -24,7 +24,13 @@
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
 
-    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
+    #if $reference_source.batchmode.processmode == 'merge':
+        #set $input_bamfiles = $reference_source.batchmode.input_bams
+    #else:
+        #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
+    #end if
+
+    #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
         ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
         ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
     #end for
@@ -43,7 +49,7 @@
         printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
     #else
         ##divide up the regions in the bam file for efficient processing
-        #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
+        #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
             samtools view -H b_${bam_count}.bam |
             grep "^@SQ" |
             cut -f 2- |
@@ -53,8 +59,6 @@
         #end for
     #end if
 
-
-
     sort -u regions_all.bed > regions_uniq.bed &&
     ## split into even small chunks, this has some disatvantages and will not be used for the moment
     ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
@@ -76,7 +80,7 @@
 
         --region '\$i'
 
-        #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
+        #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
             --bam 'b_${bam_count}.bam'
         #end for
         --fasta-reference '${reference_fasta_filename}'
@@ -283,17 +287,16 @@
                 <option value="history">History</option>
             </param>
             <when value="cached">
-                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
-                    <validator type="unspecified_build" />
-                    <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
-                </param>
+                <expand macro="input_bam">
+                    <expand macro="validation" />
+                </expand>
                 <param name="ref_file" type="select" label="Using reference genome">
-                  <options from_data_table="fasta_indexes"></options>
+                  <options from_data_table="fasta_indexes" />
                   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                 </param>
             </when>
             <when value="history"> <!-- FIX ME!!!! -->
-                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
+                <expand macro="input_bam" />
                 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
                        help="You can upload a FASTA sequence to the history and use it as reference" />
             </when>
@@ -646,6 +649,7 @@
     <tests>
         <test>
             <param name="reference_source_selector" value="history" />
+            <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="simple"/>
@@ -653,6 +657,7 @@
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
+            <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="naive_w_filters"/>
@@ -661,6 +666,7 @@
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
+            <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="naive_w_filters"/>
@@ -669,6 +675,7 @@
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
+            <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
             <param name="options_type_selector" value="full"/>