--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,56 @@
+<macros>
+    <token name="@DEPENDENCY_VERSION@">1.3.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{1207.3907,
+                    Author = {Erik Garrison},
+                    Title = {Haplotype-based variant detection from short-read sequencing},
+                    Year = {2012},
+                    Eprint = {arXiv:1207.3907},
+                    url = {http://arxiv.org/abs/1207.3907}
+                }
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+    <xml name="validation">
+        <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." />
+    </xml>
+    <xml name="input_bam">
+        <conditional name="batchmode">
+            <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF dataset for each input BAM dataset. Selecting the merge option will produce one VCF dataset for all input BAM datasets" display="radio">
+                <option value="individual" selected="true">Run individually</option>
+                <option value="merge">Merge output VCFs</option>
+            </param>
+            <when value="individual">
+                <param name="input_bams" type="data" format="bam" label="BAM dataset">
+                    <yield />
+                </param>
+            </when>
+            <when value="merge">
+                <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)">
+                    <yield />
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@COVERAGE@">
+        --min-coverage ${coverage_options.min_coverage}
+        --skip-coverage ${coverage_options.skip_coverage}
+        --limit-coverage ${coverage_options.limit_coverage}
+    </token>
+    <xml name="par_min_cov">
+        <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
+        <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
+        <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
+    </xml>
+</macros>