--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igvtools_sort.xml	Tue Jan 17 21:53:25 2012 -0500
@@ -0,0 +1,80 @@
+<tool id="igvtools_sort" name="IGVtools sort" version="1.0">
+  <description>input file by start position</description>
+  <command interpreter="bash">igvtools sort -t .
+    ## IGVTools relies on the file extension to determine format
+    #if $input.datatype.file_ext == 'vcf':
+       #set $input_name='input_file.vcf'
+       #set $output_name='output.vcf'
+    #elif $input.datatype.file_ext == 'sam':
+       #set $input_name='input_file.sam'
+       #set $output_name='output.sam'
+    #elif $input.datatype.file_ext == 'bed':
+       #set $input_name='input_file.bed'
+       #set $output_name='output.bed'
+    #elif $input.datatype.file_ext == 'psl':
+       #set $input_name='input_file.psl'
+       #set $output_name='output.psl'
+    #elif $input.datatype.file_ext == 'igv':
+       #set $input_name='input_file.igv'
+       #set $output_name='output.igv'
+    #elif $input.datatype.file_ext == 'igv.cn':
+       #set $input_name='input_file.cn'
+       #set $output_name='output.cn'
+    #end if
+    `ln -s $input  $input_name; echo $input_name` $output_name
+  </command>
+  <inputs>
+    <param name="input" type="data" format="sam,bed,vcf,psl,igv,igv.cn," label="Input file SAM,BED,VCF format"
+           help="Use samtools or picard to sort bam files"/>
+  </inputs>
+  <outputs>
+    <data format_source="input" name="output_sam" metadata_source="input" label="${tool.name} on ${on_string}: igv.sam" from_work_dir="output.sam">
+      <filter>(input.datatype.file_ext == 'sam')</filter>
+    </data>
+    <data format_source="input" name="output_bed" metadata_source="input" label="${tool.name} on ${on_string}: igv.bed" from_work_dir="output.bed">
+      <filter>(input.datatype.file_ext == 'bed')</filter>
+    </data>
+    <data format_source="input" name="output_vcf" metadata_source="input" label="${tool.name} on ${on_string}: igv.vcf" from_work_dir="output.vcf">
+      <filter>(input.datatype.file_ext == 'vcf')</filter>
+    </data>
+    <data format_source="input" name="output_psl" metadata_source="input" label="${tool.name} on ${on_string}: igv.vcf" from_work_dir="output.psl">
+      <filter>(input.datatype.file_ext == 'psl')</filter>
+    </data>
+    <data format_source="input" name="output_igv" metadata_source="input" label="${tool.name} on ${on_string}: igv" from_work_dir="output.igv">
+      <filter>(input.datatype.file_ext == 'igv')</filter>
+    </data>
+    <data format_source="input" name="output_cn" metadata_source="input" label="${tool.name} on ${on_string}: igv.cn" from_work_dir="output.cn">
+      <filter>(input.datatype.file_ext == 'igv.cn')</filter>
+    </data>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+**What it does**
+
+The IGVTools_ sort command sorts the input file by start position, as required.
+
+.. _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: .cn, .igv, .sam, .aligned, .psl, .bed, and .vcf.
+
+------
+
+**Outputs**
+
+The output will have the same format as the input file.
+
+  </help>
+</tool>