--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_cnv.xml	Wed Jul 06 07:01:20 2016 -0400
@@ -0,0 +1,176 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
+    <macros>
+        <token name="@EXECUTABLE@">cnv</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@
+
+bcftools @EXECUTABLE@
+
+--output-dir cnv_tmp
+
+## General section
+#set $section = $sec_general
+#if $section.control_sample:
+  --control-sample "${section.control_sample}"
+#end if
+#if $section.query_sample:
+  --query-sample "${section.query_sample}"
+#end if
+@AF_FILE@
+
+#if $section.plot_threshold:
+  --plot-threshold "${section.plot_threshold}"
+#end if
+
+## HMM section
+#set $section = $sec_hmm
+#if $section.aberrant_query or $section.aberrant_control:
+  #set $query_val = #if $section.aberrant_query then $section.aberrant_query else '1.0'#
+  #set $control_val = #if $section.aberrant_control then $section.aberrant_control else '1.0'#
+  --aberrant "${query_val},${control_val}"
+#end if
+#if $section.BAF_weight:
+  --BAF-weight "${section.BAF_weight}"
+#end if
+#if $section.BAF_dev_query or $section.BAF_dev_control:
+  #set $query_val = #if $section.BAF_dev_query then $section.BAF_dev_query else '1.0'#
+  #set $control_val = #if $section.BAF_dev_control then $section.BAF_dev_control else '1.0'#
+  --BAF-dev "${query_val},${control_val}"
+#end if
+#if $section.LRR_weight:
+  --LRR-weight "${section.LRR_weight}"
+#end if
+#if $section.LRR_dev_query or $section.LRR_dev_control:
+  #set $query_val = #if $section.LRR_dev_query then $section.LRR_dev_query else '1.0'#
+  #set $control_val = #if $section.LRR_dev_control then $section.LRR_dev_control else '1.0'#
+  --LRR-dev "${query_val},${control_val}"
+#end if
+#if $section.LRR_smooth_win:
+  --LRR-smooth-win "${section.LRR_smooth_win}"
+#end if
+#if $section.optimize:
+  --optimize "${section.optimize}"
+#end if
+#if $section.same_prob:
+  --same-prob "${section.same_prob}"
+#end if
+#if $section.err_prob:
+  --err-prob "${section.err_prob}"
+#end if
+#if $section.xy_prob:
+  --xy-prob "${section.xy_prob}"
+#end if
+
+## Filter section
+#set $section = $sec_restrict
+@REGIONS@
+@TARGETS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+&& mv $output_dir/cn.*.tab "$output_cn"
+&& mv $output_dir/dat.*.tab "$output_dat"
+&& mv $output_dir/summary.*.tab "$output_summary"
+## && python $output_dir/plot.*.py
+]]>
+    </command>
+    <inputs>
+        <param name="output_dir" type="hidden" value="cnv_tmp"/>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+        </section>
+        <param name="reference_fasta" type="data" format="fasta" label="Reference Fasta" />
+        <section name="sec_general" expanded="true" title="General Options">
+            <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query samply name" />
+            <param name="control_sample" type="text" label="Control Sample" optional="True" help="Optional control sample name to highlight differences" />
+            <expand macro="macro_AF_file" />
+            <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" />
+        </section>
+        <section name="sec_hmm" expanded="false" title="HMM Options">
+            <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
+            <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" >
+                <help>
+                  Iteratively estimate the fraction of aberrant cells, down to the given fraction. 
+                  Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
+                </help>
+            </param>
+            <param name="same_prob" type="float" value="" min="0." max="1." label="Same Prob" optional="True">
+                <help>
+                    The prior probability of the query and the control sample being the same. 
+                    Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
+                </help>
+            </param>
+            <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True">
+                <help>
+                    The HMM probability of transition to another copy number state. 
+                    Increasing this value leads to smaller and more frequent calls. 
+                </help>
+            </param>
+
+            <param name="aberrant_query" type="float" value="" min="0." max="1." label="Aberrant Query" optional="true" 
+                   help="Fraction of aberrant cells in query, defaults to 1." />
+            <param name="aberrant_control" type="float" value="" min="0." max="1." label="Aberrant Control" optional="true" 
+                   help="Fraction of aberrant cells in control, defaults to 1." />
+            <param name="BAF_weight" type="float" value="1." min="0." max="1." label="Baf Weight" optional="True" help="relative contribution from BAF" />
+
+            <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true" 
+                   help="Expected BAF deviation in query, defaults to: 0.04" />
+            <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" 
+                   help="Expected BAF deviation in control, defaults to: 0.04" />
+
+            <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" >
+                <help>
+                    Relative contribution from LRR.  
+                    With noisy data, this option can have big effect on the number of calls produced. 
+                    In truly random noise (such as in simulated data), the value should be set high (1.0), i
+                    but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).
+                </help>
+            </param>
+            <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation" 
+                   help="Expected LRR deviation in query, default is: 0.2" />
+            <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" 
+                   help="Expected LRR deviation in control, default is: 0.2" />
+            <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True" 
+                   help="Window of LRR moving average smoothing" />
+
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_cn" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.cn"/>
+        <data name="output_dat" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.dat"/>
+        <data name="output_summary" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.summary"/>
+        <!-- add plot output -->
+        <!-- script has png per chr, html of images or collect into pdf?
+        <data name="output_plots" format="" />
+         -->
+    </outputs>
+    <tests />
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR). 
+The HMM considers the following copy number states: CN 2 (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>