--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_stats.xml	Wed Jul 06 07:09:13 2016 -0400
@@ -0,0 +1,147 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
+    <macros>
+        <token name="@EXECUTABLE@">stats</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILES@
+#set $section = $sec_restrict
+@PREPARE_TARGETS_FILE@
+## Stats section
+#set $section = $sec_default
+@PREPARE_FASTA_REF@
+@PREPARE_EXONS_FILE@
+
+bcftools @EXECUTABLE@
+
+## Stats section
+#set $section = $sec_default
+@FASTA_REF@
+@EXONS_FILE@
+${section.first_allele_only}
+#if $section.depth.set_depth == 'yes':
+  --depth "${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}"
+#end if
+#if $section.user_tstv:
+  --user-tstv "${section.user_tstv}"
+#end if
+#if len($input_vcfs) == 1:
+${section.split_by_ID}
+#end if
+${section.verbose}
+
+## Stats section
+#set $section = $sec_restrict
+@APPLY_FILTERS@
+@COLLAPSE@
+@REGIONS@
+@SAMPLES@
+@TARGETS@
+@INCLUDE@
+@EXCLUDE@
+
+## Primary Input/Outputs
+@INPUT_FILES@
+> $output_file
+## requires: matplotlib and pdflatex
+#if $plot_title:
+&& plot-vcfstats -p 'plot_tmp/' -T $plot_title -s $output_file
+#end if
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_inputs" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_samples" />
+            <expand macro="macro_apply_filters" />
+            <expand macro="macro_collapse" />
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <section name="sec_default" expanded="true" title="Stats Options">
+            <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only" 
+                   help="Include only 1st allele at multiallelic sites" />
+            <conditional name="depth">
+                <param name="set_depth" type="select" label="depth distribution: min,max,bin_size [0,500,1]">
+                    <option value="no">use depth defaults</option>
+                    <option value="yes">set depth</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
+                    <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 
+                    <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
+                    <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
+                </when>
+            </conditional>
+            <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="Reference sequence" />
+            <expand macro="macro_exons_file" />
+            <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 
+                   help="Collect stats for sites with ID separately (known vs novel)" />
+            <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 
+                   help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
+                  <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
+
+            </param>
+            <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose" 
+                   help="Produce verbose per-site and per-sample output" />
+        </section>
+        <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
+            <validator type="regex" message="">^\w.*\w$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="txt"/>
+        <data name="output_pdf" format="pdf">
+            <filter>plot_title</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_files" ftype="vcf" value="stats.b.vcf,stats.a.vcf" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
+                    <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_files" ftype="vcf" value="mpileup.vcf" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
+                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
+                    <has_text_matching expression="ST\t0\tA>C\t16"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. 
+
+When two files are given, the program generates separate stats for intersection and the complements. 
+By default only sites are compared, -s/-S must given to include also sample columns.
+
+@COLLAPSE_HELP@
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+</help>
+    <expand macro="citations" />
+</tool>