<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>