--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_phase.xml	Thu Mar 27 15:26:17 2014 -0400
@@ -0,0 +1,138 @@
+<tool id="samtools_phase" name="Call and phase" version="1.0.0">
+    <description>heterozygous SNPs</description>
+    <requirements>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+    </requirements>
+    <command>samtools phase -b "phase_wrapper"
+        #if str($option_set.option_sets) == 'advanced':
+            ${option_set.ignore_chimeras}
+            -k $option_set.block_length
+            -q $option_set.min_het
+            -Q $option_set.min_bq
+            -D $option_set.read_depth
+            ${option_set.drop_ambiguous}
+        #else
+            -k 13 -q 37 -Q 13 -D 256
+        #end if
+        "$input_bam" &gt; "$phase_sets"
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <inputs>
+        <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
+        <conditional name="option_set">
+            <param name="option_sets" type="select" label="Phase parameters">
+                <option value="default">Use defaults</option>
+                <option value="advanced">Advanced options</option>
+            </param>
+            <when value="default" />
+            <when value="advanced">
+                <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" />
+                <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
+                <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" />
+                <param name="read_depth" type="integer" value="256" label="Read depth" />
+                <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
+                <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="phase_sets" />
+        <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
+        <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
+        <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="option_sets" value="default" /> 
+            <param name="input_bam" value="samtools_phase_in_1.bam" /> 
+            <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
+            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" />
+            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" />
+            <output name="chimera" file="empty_file.bam" compare="contains" />
+        </test>
+        <test>
+            <param name="input_bam" value="samtools_phase_in_2.bam" /> 
+            <param name="option_sets" value="advanced" /> 
+            <param name="option_set|block_length" value="13" />
+            <param name="option_set|min_het" value="37" />
+            <param name="option_set|min_bq" value="13" />
+            <param name="option_set|read_depth" value="256" />
+            <param name="option_set|ignore_chimeras" value="false" />
+            <param name="option_set|drop_ambiguous" value="true" />
+            <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
+            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" />
+            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" />
+            <output name="chimera" file="empty_file.bam" compare="contains" />
+        </test>
+        <test>
+            <param name="input_bam" value="samtools_phase_in_2.bam" /> 
+            <param name="option_sets" value="advanced" /> 
+            <param name="option_set|block_length" value="13" />
+            <param name="option_set|min_het" value="37" />
+            <param name="option_set|min_bq" value="13" />
+            <param name="option_set|read_depth" value="256" />
+            <param name="option_set|ignore_chimeras" value="true" />
+            <param name="option_set|drop_ambiguous" value="false" />
+            <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
+            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" />
+            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" />
+            <output name="chimera" file="empty_file.bam" compare="contains" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Call and phase heterozygous SNPs
+    
+------
+
+.. list-table:: **Options**
+   :widths: 5 5 40 10
+   :header-rows: 1
+
+   * - Flag
+     - Type
+     - Description
+     - Default
+   * - -k
+     - INT
+     - Block length
+     - 13
+   * - -b
+     - STR
+     - Prefix of BAM file output
+     - *null*
+   * - -q
+     - INT
+     - Minimum het phred-LOD
+     - 37
+   * - -Q
+     - INT
+     - Min base quality in het calling
+     - 13
+   * - -D
+     - INT
+     - Max read depth
+     - 256
+   * - -D
+     - BOOLEAN
+     - Do not attempt to fix chimeras
+     - *off*
+   * - -A
+     - BOOLEAN
+     - Drop reads with ambiguous phase
+     - *off*
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+        </help>
+</tool>