--- a/bcftools_mpileup.xml	Tue Dec 12 14:05:31 2017 -0500
+++ b/bcftools_mpileup.xml	Thu Feb 21 16:09:57 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
     <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
@@ -16,7 +16,7 @@
             <option value="256">The alignment or this read is not primary</option>
             <option value="512">The read fails platform/vendor quality checks</option>
             <option value="1024">The read is a PCR or optical duplicate</option>
-         </xml>
+        </xml>
     </macros>
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
@@ -37,9 +37,9 @@
     #silent $bam_list.append($input_name)
     ln -s '${input.input_bam}' ${input_name} &&
     #if $input.input_bam.ext == 'bam':
-      ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
+        ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
     #else:
-      ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
+        ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
     #end if
 #else:
     #for $bam_count, $input_bam in enumerate( $input.input_bams ):
@@ -59,11 +59,11 @@
 
 #set $input_fa_ref = None
 #if $reference_source.reference_source_selector == "history":
-  #set $input_fa_ref = 'ref.fa'
-  ln -s '${reference_source.ref_file}' $input_fa_ref &&
-  samtools faidx $input_fa_ref &&
+    #set $input_fa_ref = 'ref.fa'
+    ln -s '${reference_source.ref_file}' $input_fa_ref &&
+    samtools faidx $input_fa_ref &&
 #elif $reference_source.reference_source_selector == "cached":
-  #set $input_fa_ref = $reference_source.ref_file.fields.path
+    #set $input_fa_ref = $reference_source.ref_file.fields.path
 #end if
 
 #set $section = $sec_restrict
@@ -81,53 +81,53 @@
 ## Indel Calling section
 #set $section = $sec_indel
 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
-  --skip-indels
+    --skip-indels
 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
-  -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
-  -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
-  -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
-  -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
-  -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
-  --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
-  -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
-  ${section.perform_indel_calling.gapped_read_per_sample}
-  #if len( $section.perform_indel_calling.platform_list_repeat ):
-    -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
-  #end if
+    -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
+    -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
+    -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
+    -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
+    -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
+    --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
+    -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
+    ${section.perform_indel_calling.gapped_read_per_sample}
+    #if len( $section.perform_indel_calling.platform_list_repeat ):
+        -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
+    #end if
 #end if
 
 ## Filter section
 #set $section = $sec_filtering
 #if str( $section.filter_by_flags.filter_flags ) == "filter":
-  #if $section.filter_by_flags.require_flags:
-    --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
-  #end if
-  #if $section.filter_by_flags.exclude_flags:
-    --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
-  #end if
+    #if $section.filter_by_flags.require_flags:
+        --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
+    #end if
+    #if $section.filter_by_flags.exclude_flags:
+        --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
+    #end if
 #end if
 -d "${section.max_reads_per_bam}"
 ${section.skip_anomalous_read_pairs}
 #if str( $section.quality.quality_settings ) == "adjust":
-  $section.quality.baq
-  -q "${section.quality.minimum_mapping_quality}"
-  -Q "${section.quality.minimum_base_quality}"
-  -C "${section.quality.coefficient_for_downgrading}"
+    $section.quality.baq
+    -q "${section.quality.minimum_mapping_quality}"
+    -Q "${section.quality.minimum_base_quality}"
+    -C "${section.quality.coefficient_for_downgrading}"
 #end if
 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
-  --ignore-RG
+    --ignore-RG
 #elif str( $section.read_groups.read_groups_selector ) == "paste":
-  -G "${section.read_groups.rg_action}${read_groups_file}"
+    -G "${section.read_groups.rg_action}${read_groups_file}"
 #elif str( $section.read_groups.read_groups_selector ) == "history"
-  -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
+    -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
 #end if
 
 #set $section = $sec_output_options
 #if $section.output_tags:
- --annotate "$section.output_tags"
+    --annotate "$section.output_tags"
 #end if
 #if $section.gvcf:
- --gvcf "$section.gvcf"
+    --gvcf "$section.gvcf"
 #end if
 
 ## Subset section
@@ -147,18 +147,17 @@
 #echo ' '.join($bam_list)#
 > '$output_file'
 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
-&& echo 'read-groups:'
-&& cat ${read_groups_file}
+    && echo 'read-groups:'
+    && cat ${read_groups_file}
 #end if
-]]>
-    </command>
+    ]]></command>
     <configfiles>
         <configfile name="read_groups_file">
 <![CDATA[#slurp
 #set pasted_data = ''
 #set $section = $sec_filtering
 #if str( $section.read_groups.read_groups_selector ) == "paste":
-  #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
+    #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
 #end if
 #slurp
 ${pasted_data}
@@ -444,7 +443,6 @@
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
 @BCFTOOLS_WIKI@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>