--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_roh.xml	Wed Jul 06 07:08:58 2016 -0400
@@ -0,0 +1,119 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>HMM model for detecting runs of autozygosity</description>
+    <macros>
+        <token name="@EXECUTABLE@">roh</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@
+## General section
+#set $section = $sec_general
+@PREPARE_AF_FILE@
+
+bcftools @EXECUTABLE@
+
+## General section
+#set $section = $sec_general
+@SAMPLE@
+@AF_FILE@
+#if $section.AF_tag:
+  --AF-tag "${section.AF_tag}"
+#end if
+#if $section.AF_dflt:
+  --AF-dflt "${section.AF_dflt}"
+#end if
+@ESTIMATE_AF@
+#if $section.GTs_only:
+  --GTs-only "${section.GTs_only}"
+#end if
+${section.skip_indels}
+#if $section.genetic_map:
+  --genetic-map "${section.genetic_map}"
+#end if
+#if $section.rec_rate:
+  --rec-rate "${section.rec_rate}"
+#end if
+
+## HMM section
+#set $section = $sec_hmm
+#if $section.hw_to_az:
+  --hw-to-az "${section.hw_to_az}"
+#end if
+#if $section.az_to_hw:
+  --az-to-hw "${section.az_to_hw}"
+#end if
+${section.viterbi_training}
+
+## General section
+#set $section = $sec_restrict
+@REGIONS@
+@TARGETS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+> "$output_file"
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+        </section>
+        <section name="sec_general" expanded="true" title="Roh General Options">
+            <expand macro="macro_sample" />
+            <param name="AF_tag" type="text" value="" label="AF TAG"  optional="True" 
+                   help="Use the specified INFO tag TAG as an allele frequency estimate instead of the defaul AC and AN tags. Sites which do not have TAG will be skipped." />
+            <param name="AF_dflt" type="float" value="" min="0." max="1." label="AF Default" optional="True" help="If AF is not known, use this allele frequency" />
+            <expand macro="macro_AF_file" />
+            <expand macro="macro_estimate_AF" />
+            <param name="GTs_only" type="float" label="Gts Only" optional="True" help="Use GTs, ignore PLs, use &lt;float&gt; for PL of unseen genotypes. Safe value to use is 30 to account for GT errors." />
+            <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
+            <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
+            <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
+        </section>
+        <section name="sec_hmm" expanded="true" title="HMM Options">
+            <param name="hw_to_az" type="float" label="Hw To Az" default="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
+            <param name="az_to_hw" type="float" label="Az To Hw" default="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
+            <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="tabular"/>
+    </outputs>
+    <tests>
+        <!-- Need an actual test input file -->
+        <test>
+            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
+            <param name="sample" value="HG00100" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="HG00100"/>
+                    <has_text text="State "/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+HMM model for detecting runs of autozygosity.
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+   </help>
+    <expand macro="citations" />
+</tool>