--- a/depth_of_coverage.xml	Mon Aug 25 17:44:53 2014 -0400
+++ b/depth_of_coverage.xml	Mon Jun 04 05:38:15 2018 -0400
@@ -1,18 +1,14 @@
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
   <description>on BAM files</description>
-  <expand macro="requirements" />
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
   <command interpreter="python">gatk2_wrapper.py
    ##--max_jvm_heap_fraction "1"
    --stdout "${output_log}"
-   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
-       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-           -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
-       #end if
-   #end for
+   @BAM_INPUTS@
    -p '
    @JAR_PATH@
     -T "DepthOfCoverage"
@@ -32,13 +28,13 @@
         #end for
     #end if
     --out "${output_per_locus_coverage}"
-    
+
     #for $ct_group in $summary_coverage_threshold_group:
         --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
     #end for
     --outputFormat "${output_format}"
    '
-   
+
     #include source=$standard_gatk_options#
     ##start analysis specific options
     #if $analysis_param_type.analysis_param_type_selector == "advanced":
@@ -84,7 +80,7 @@
             &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
         #end if
     #end if
-    
+
     #if 'readgroup' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
         #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
             &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
@@ -103,7 +99,7 @@
             &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
         #end if
     #end if
-    
+
     #if 'library' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ):
         #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
             &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
@@ -122,54 +118,47 @@
             &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
         #end if
     #end if
-    
 
   </command>
   <inputs>
     <conditional name="reference_source">
       <expand macro="reference_source_selector_param" />
       <when value="cached">
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-            </param>
-        </repeat>
+        <expand macro="input_bams_cached" />
         <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
           <options from_data_table="gatk2_picard_indexes">
-            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
+            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
           </options>
           <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!!!! -->
-        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
-            <param name="input_bam" type="data" format="bam" label="BAM file" />
-        </repeat>
+
+        <expand macro="input_bams_history" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
-    
+
     <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
-    
+
     <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;gt;">
       <option value="sample" selected="True">sample</option>
       <option value="readgroup">readgroup</option>
       <option value="library">library</option>
     </param>
-    
+
     <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
         <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
     </repeat>
-    
+
     <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
       <option value="csv">csv</option>
       <option value="table">table</option>
       <option value="rtable" selected="True">rtable</option>
     </param>
-    
+
     <expand macro="gatk_param_type_conditional" />
-    
+
     <expand macro="analysis_type_conditional">
         <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
         <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
@@ -358,7 +347,7 @@
             </conditional>
         </actions>
     </data>
-    
+
     <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
         <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
         <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
@@ -511,7 +500,7 @@
             </conditional>
         </actions>
     </data>
-    
+
     <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
         <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
         <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
@@ -664,7 +653,7 @@
             </conditional>
         </actions>
     </data>
-    
+
     <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
   </outputs>
   <trackster_conf/>
@@ -690,7 +679,7 @@
   <help>
 **What it does**
 
-DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. 
+DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score.
 
 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html&gt;`_.