--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/genetrack.xml	Tue Nov 17 14:19:45 2015 -0500
@@ -0,0 +1,111 @@
+<?xml version="1.0"?>
+<tool id="genetrack" name="Genetrack" version="@WRAPPER_VERSION@.0">
+    <description>peak predictor</description>
+    <macros>
+        <import>genetrack_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+        python $__tool_directory__/genetrack.py
+        --input_format $input_format_cond.input_format
+        #if str($input_format_cond.input_format) == "ssccidx":
+            #for $i in $input_format_cond.input_ssccidx:
+                 --input "${i}" "${i.hid}"
+            #end for
+        #elif str($input_format_cond.input_format) == "gff":
+            #for $i in $input_format_cond.input_gff:
+                 --input "${i}" "${i.hid}"
+            #end for
+        #end if
+        --sigma $sigma
+        --exclusion $exclusion
+        --up_width $up_width
+        --down_width $down_width
+        --filter $filter
+        --chunk_size $chunk_size
+    </command>
+    <inputs>
+        <conditional name="input_format_cond">
+            <param name="input_format" type="select" label="Format of files for conversion">
+                <option value="ssccidx">Genetracktool</option>
+                <option value="gff" selected="True">Gff</option>
+            </param>
+            <when value="ssccidx">
+                <param name="input_ssccidx" type="data" format="ssccidx" multiple="True" label="Predict peaks on" />
+            </when>
+            <when value="gff">
+                <param  name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" />
+            </when>
+        </conditional>
+        <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." />
+        <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." />
+        <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" />
+        <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" />
+        <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
+        <param name="chunk_size" type="integer" value="10" min="1" label="Chunk each chromosome into" help="Value is millions of base pairs where each size increment uses about 20MB of memory." />
+    </inputs>
+    <outputs>
+        <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_gff" value="genetrack_input2.gff" ftype="gff" />
+            <param name="input_format" value="gff" />
+            <param name="sigma" value="5" />
+            <param name="exclusion" value="20" />
+            <param name="up_width" value="10" />
+            <param name="down_width" value="10" />
+            <param name="filter" value="3" />
+            <param name="chunk_size" value="10" />
+            <output_collection name="genetrack_output" type="list">
+                <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_ssccidx" value="genetrack_input3.ssccidx" ftype="ssccidx" />
+            <param name="input_format" value="ssccidx" />
+            <param name="sigma" value="5" />
+            <param name="exclusion" value="20" />
+            <param name="up_width" value="10" />
+            <param name="down_width" value="10" />
+            <param name="filter" value="3" />
+            <param name="chunk_size" value="10" />
+            <output_collection name="genetrack_output" type="list">
+                <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" />
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_gff" value="genetrack_input_unsorted4.gff" ftype="gff" />
+            <param name="input_format" value="gff" />
+            <param name="sigma" value="5" />
+            <param name="exclusion" value="20" />
+            <param name="up_width" value="10" />
+            <param name="down_width" value="10" />
+            <param name="filter" value="3" />
+            <param name="chunk_size" value="10" />
+            <output_collection name="genetrack_output" type="list">
+                <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" />
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Genetrack takes a standard set of data on both the sense and antisense strands and smooths their relative reads.
+It then calls the peaks present in the smoothed dataset and uses those peak locations to calculate the final
+reads from surrounding reads.  Finally, it ensures each peak is above a threshold and that two peaks are not
+too close to each other.
+
+**Options**
+
+* **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.
+* **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called.
+* **Upstream width of called peaks** - Upstream width of called peaks.
+* **Downstream width of called peaks** - Downstream width of called peaks.
+* **Filter** - Absolute read filter.  Restricts output to only peaks with larger peak height.
+* **Chunk each chromosome into** - Size, in millions of base pairs, to chunk each chromosome when processing.  Each 1 million size uses approximately 20MB of memory.
+    </help>
+    <expand macro="citations" />
+</tool>