--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_merge.xml	Wed Jul 06 07:04:14 2016 -0400
@@ -0,0 +1,165 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
+    <macros>
+        <token name="@EXECUTABLE@">merge</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILES@
+bcftools @EXECUTABLE@
+
+## Header section
+#set $section = $sec_header
+${section.print_header}
+#if $section.use_header:
+  --use-header "${section.use_header}"
+#end if
+
+## Merge section
+#set $section = $sec_merge
+${section.force_samples}
+
+#if $section.info_rules:
+  --info-rules "${section.info_rules}"
+#end if
+
+#if $section.merge:
+  --merge "${section.merge}"
+#end if
+
+#set $section = $sec_restrict
+@APPLY_FILTERS@
+@REGIONS@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILES@
+> "$output_file"
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_inputs" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_apply_filters" />
+            <expand macro="macro_regions" />
+        </section>
+        <section name="sec_merge" expanded="true" title="Merge Options">
+            <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" help="Resolve duplicate sample names" />
+            <param name="info_rules" type="text" label="Info Rules" help="Rules for merging INFO fields (method is one of sum,avg,min,max,join) or &quot;-&quot; to turn off the default [DP:sum,DP4:sum]" />
+            <param name="merge" type="select" label="Merge" optional="True" 
+                  help="Allow multiallelic records for: snps|indels|both|all|none|id, see man page for details [both]" >
+                  <option value="none">none - no new multiallelics, output multiple records instead</option>
+                  <option value="snps">snps - allow multiallelic SNP records</option>
+                  <option value="indels">indels - allow multiallelic indel records</option>
+                  <option value="both">both - both SNP and indel records can be multiallelic</option>
+                  <option value="all">all - SNP records can be merged with indel records</option>
+                  <option value="id">id - merge by ID</option>
+            </param>
+        </section>
+        <section name="sec_header" expanded="false" title="Header Options">
+          <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
+          <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header" help="Print only the merged header and exit" />
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.a.vcf,merge.b.vcf,merge.c.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="3000150" />
+                    <has_text text="3188209" />
+                    <has_text_matching expression="\tq10;q20\t[\s]*INDEL"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="merge" value="none" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="1\t3000000\t.\tC\tCCG\t"/>
+                    <has_text_matching expression="1\t3000000\t.\tC\tG\t"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="merge" value="both" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="1\t3000150\t\.\tC\t(A,G|G,A)\t"/>
+                    <has_text_matching expression="1\t3106154\t\.\tC\t(CC,CCC|CCC,CC)\t"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.2.a.vcf,merge.2.b.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="merge" value="all" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="1\t3000000\t\.\tC\t(CCG,G|G,CCG)\t"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.3.a.vcf,merge.3.b.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="info_rules" value="TR:sum,TA:sum,TG:sum" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/>
+                    <has_text_matching expression="TR=[^;\t]*11"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
+            <param name="force_samples" value="true" />
+            <param name="merge" value="id" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+
+Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file. 
+
+Note that only records from different files can be merged, never from the same file. 
+For "vertical" merge take a look at "bcftools norm" instead.
+
+@REGIONS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>