--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,74 @@
+<?xml version='1.0' encoding='utf-8'?>
+<macros>
+  <token name="@VERSION@">1.2</token>
+  <xml name="requirements">
+    <requirements>
+      <!-- This requirement handles also bcftools from BioConda channel => https://github.com/bioconda/bioconda-recipes/tree/60d2ea750430dbe0191f6f8d5639f90fc1223bd9/recipes/bcftools/1.2 -->
+      <requirement type="package" version="1.2">bcftools</requirement>
+    </requirements>
+  </xml>
+  <xml name="version_command">
+      <version_command><![CDATA[bcftools 2>&1 | grep 'Version:']]></version_command>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1093/bioinformatics/btp352</citation>
+      <yield />
+    </citations>
+  </xml>
+  <xml name="macro_exclude">
+    <param name="exclude" label="Exclude" help="exclude sites for which the expression is true (see man page for details)" />
+  </xml>
+  <xml name="macro_collapse">
+      <param name="collapse" label="Collapse" type="select" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
+        <option value="snps">snps</option>
+        <option value="indels">indels</option>
+        <option value="both">both</option>
+        <option value="all">all</option>
+        <option value="some">some</option>
+        <option value="none" selected="True">None</option>
+    </param>
+  </xml>
+  <xml name="macro_apply_filters_repeat">
+    <repeat name="apply_filters_repeat" title="Apply Filters">
+      <param name="apply_filters" label="Apply Filters" help="require at least one of the listed FILTER strings (e.g. &quot;PASS,.&quot;)" />
+    </repeat>
+  </xml>
+
+  <token name="@SEC_DEF_REGIONS@">
+#if $sec_default.regions_file:
+  --regions-file "${sec_default.regions_file}"
+#end if
+  </token>
+  <token name="@SEC_DEF_TARGETS@">
+#if $sec_default.targets_file:
+  --targets-file "${sec_default.targets_file}"
+#end if
+  </token>
+  <token name="@SEC_DEF_SAMPLES@">
+#if $sec_default.samples_file:
+  --samples-file "${sec_default.samples_file}"
+#end if
+  </token>
+
+  <xml name="macro_samples">
+    <param name="samples_file" label="Samples File" type="data" format="data" optional="True" help="file of samples to include" />
+    <param name="invert_samples_file" label="Invert Samples" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the sample file selection" />
+  </xml>
+  <xml name="macro_targets">
+    <param name="targets_file" label="Targets File" type="data" format="data" optional="True" help="similar to -R but streams rather than index-jumps" />
+    <param name="invert_targets_file" label="Invert Targets" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the target file selection" />
+  </xml>
+  <xml name="macro_regions">
+    <param name="regions_file" label="Regions File" type="data" format="data" optional="True" help="restrict to regions listed in a file" />
+    <param name="invert_regions_file" label="Invert Regions" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by region file selection" />
+  </xml>
+  <xml name="macro_select_output_type">
+    <param name="select_output_type" type="select">
+      <option value="v" selected="True">uncompressed VCF</option>
+      <option value="z">compressed VCF</option>
+      <option value="u">uncompressed BCF</option>
+      <option value="b">compressed BCF</option>
+    </param>
+  </xml>
+</macros>