--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin_frameshifts.xml	Wed Jun 05 13:05:06 2019 -0400
@@ -0,0 +1,100 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1">
+    <description>plugin Annotate frameshift indels</description>
+    <macros>
+        <token name="@EXECUTABLE@">frameshifts</token>
+        <token name="@PLUGIN_ID@">frameshifts</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILE@
+#set $section = $sec_restrict
+@PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
+## exons file needs to be bgzip and have tabix index
+bgzip -c $exons > exons.bed.gz &&
+tabix exons.bed.gz &&
+
+bcftools plugin @EXECUTABLE@
+## VCF input section
+#set $section = $sec_restrict
+@INCLUDE@
+@EXCLUDE@
+@REGIONS@
+@TARGETS@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+## Plugin options
+-- --exons exons.bed.gz
+> '$output_file'
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <param name="exons" type="data" format="bed"
+        label="Exons File" help="BED file describing exons" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_restrict" />
+            <expand macro="macro_restrict" type="target" label_type="Target" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
+            <param name="exons" ftype="bed" value="plugin_frameshifts.bed" />
+            <param name="output_type" value="v" />
+            <output name="output_file" ftype="vcf">
+                <assert_contents>
+                    <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
+                    <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" />
+                    <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+A simple tool to annotate the effect of indel variants.
+
+Adds an ``OOF`` (out-of-frame) subfield to the ``INFO`` field of indel records
+found in the input, where
+
+- ``OOF=1`` indicates that the indel results in a frameshift
+- ``OOF=0`` indicates an in-frame indel
+
+The information about indel effects is extracted from the ``BED`` input, which
+is supposed to describe the reference genome exons.
+
+If a variant record lists several ``ALT`` alleles, some of them indels, then
+``OOF`` will be a comma-separated list of status indicators. In the list a
+third ``OOF`` status code of ``-1`` will be used to indicate ``ALT`` alleles
+that are not associated with a change in sequence length or that don't affect
+an exon.
+
+The formal definition (added to the VCF header) of the ``OOF`` subfield is::
+
+  INFO=<ID=OOF,Number=A,Type=Integer,Description="Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)">
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>