--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igvtools_tile.xml	Tue Jan 17 21:53:25 2012 -0500
@@ -0,0 +1,125 @@
+<tool id="igvtools_tile" name="IGVtools tile" version="1.0">
+  <description>convert a sorted data input file to a binary tiled data (.tdf) file</description>
+  <command interpreter="bash">igvtools tile 
+    #if $zoom.__str__ != '':
+      -z $zoom
+    #end if
+    #if $window_functions.__str__ != '':
+      -f '$window_functions'
+    #end if
+    #if $probe.__str__ != '':
+      -p '$probe'
+    #end if
+    ## IGVTools relies on the file extension to determine format
+    #if $input.datatype.file_ext == 'wig':
+       #set $input_name='input_file.wig'
+    #elif $input.datatype.file_ext == 'igv.snp':
+       #set $input_name='input_file.snp'
+    #elif $input.datatype.file_ext == 'igv.gct':
+       #set $input_name='input_file.gct'
+    #elif $input.datatype.file_ext == 'igv.cn':
+       #set $input_name='input_file.cn'
+    #elif $input.datatype.file_ext == 'igv':
+       #set $input_name='input_file.igv'
+    #end if
+    `ln -s $input  $input_name; echo $input_name` $output_tdf $refGenomeSource.ref
+  </command>
+  <inputs>
+    <conditional name="refGenomeSource">
+      <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
+        <option value="built-in">Use a built-in reference</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="built-in">
+        <param name="ref" type="select" label="Select a reference genome">
+          <options from_file="igv_indices.loc">
+            <column name="dbkey" index="0" />
+            <column name="name" index="1" />
+            <column name="value" index="2" />
+            <filter type="sort_by" column="1" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ref" type="data" format="igv.genome" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <param name="input" type="data" format="wig,igv,igv.cn,igv.snp,igv.gct" label="Input file" help="The input WIG,CN,IGV,GCT,SNP feature file"/>
+    <param name="zoom" type="integer" value="7" optional="true" label="-z maximum zoom level to precompute" 
+           help="The default value is 7 and is sufficient for most files. To reduce file
+               size at the expense of IGV performance this value can be reduced." />
+    <param name="window_functions" type="select" display="checkboxes" multiple="True" label="-f Functions to calculate over windows" 
+           help="If none are selected, will default to mean">
+        <option value="mean" selected="true">mean</option>
+        <option value="min">min</option>
+        <option value="max">max</option>
+    </param>
+    <param name="probe" type="data" format="bed" optional="true" label="Probe file for GCT input" 
+           help="Specifies a bed file to be used to map probe identifiers to locations.  
+                 This option is useful when preprocessing .gct files.  
+                 The bed file should contain 4 columns:
+                   chr start end name
+                 where name is the probe name in the .gct file."/>
+  </inputs>
+  <outputs>
+    <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+**What it does**
+
+The IGVTools_ tile command converts a sorted data input file to a binary tiled data (.tdf) file. Use this command to pre-process large datasets for improved IGV performance. 
+
+.. _IGVTools: http://www.broadinstitute.org/software/igv/igvtools_commandline
+.. _IGV: http://www.broadinstitute.org/igv/
+
+------
+
+To cite your use of IGV in your publication::
+
+  James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. 
+  Integrative Genomics Viewer.  Nature Biotechnology 29, 24-26 (2011)
+
+------
+
+**Input formats**
+
+Supported input file formats are: .wig, .cn, .snp, .igv, and .gct.
+
+------
+
+**Outputs**
+
+The output format is IGV tiled data file (TDF) file (.tdf)
+
+-------
+
+
+**IGVTools count  parameter list**
+
+This is an exhaustive list of igvtools count options:
+
+For **count**::
+
+  -z Integer        Specifies the maximum zoom level to precompute. The default
+                    value is 7 and is sufficient for most files. To reduce file
+                    size at the expense of IGV performance this value can be
+                    reduced.
+  
+  -p file           Specifies a "bed" file to be used to map probe identifiers
+                    to locations.  This option is useful when preprocessing . gct
+                    files.  The bed file should contain 4 columns:
+                    chr start end name
+                    where name is the probe name in the .gct file.
+  
+  -f list           A comma delimited list specifying window functions to use
+                    when reducing the data to precomputed tiles.   Possible
+                    values are  min, max, and mean.  By default only the mean
+                    is calculated.
+
+
+  
+  </help>
+</tool>