<tool id="igvtools_count" name="IGVtools count" version="1.0">
  <description>average feature density across the genome</description>
  <command interpreter="bash">igvtools count 
    #if $zoom.__str__ != '':
      -z $zoom
    #end if
    #if $window.__str__ != '':
      -w $window
    #end if
    #if $extend.__str__ != '':
      -e $extend
    #end if
    #if $window_functions.__str__ != '':
      -f '$window_functions'
    #end if
    ## IGVTools relies on the file extension to determine format
    #if $input.datatype.file_ext == 'bam':
       #set $input_name='input_file.bam'
    #elif $input.datatype.file_ext == 'sam':
       #set $input_name='input_file.sam'
    #elif $input.datatype.file_ext == 'bed':
       #set $input_name='input_file.bed'
    #elif $input.datatype.file_ext == 'psl':
       #set $input_name='input_file.psl'
    #end if
    `ln -s $input  $input_name; echo $input_name` '$output_fmt' $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="sam,bam,bed,psl" label="Input file" help="The input BAM,SAM,BED,PSL 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" type="integer" value="25" optional="true" label="-w Window size" 
           help="The window size over which coverage is averaged. Defaults to 25 bp." />
    <param name="extend" type="integer" value="" optional="true" label="Extend feature length" 
           help="The read or feature is extended by the specified distance in bp prior to counting. 
                 This option is useful for chip-seq and rna-seq applications. The value is generally set to the
                 average fragment length of the library." />
    <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="output_fmt" type="select" display="checkboxes" multiple="True" force_select="true" label="Select output format" 
           help="If none are selected, will default to mean">
        <option value="output.tdf" selected="true">IGV tdf</option>
        <option value="output.wig">wig</option>
    </param>
  </inputs>
  <outputs>
    <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf">
      <filter>('output.tdf' in output_fmt)</filter>
    </data>
    <data format="wig" name="output_wig" metadata_source="input" label="${tool.name} on ${on_string}: igv.wig" from_work_dir="output.wig">
      <filter>('output.wig' in output_fmt)</filter>
    </data>
  </outputs>
  <tests>
  </tests>
  <help>
**What it does**

The IGVTools_ count command computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments. By default, the resulting file will be displayed as a bar chart when loaded into IGV_.

.. _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: .sam, .bam, .aligned, .psl, .pslx, and .bed.

------

**Outputs**

The output formats are IGV tiled data file (TDF) file (.tdf) and/or WIG file (.wig)

-------


**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.
  
  -w Integer        The window size over which coverage is averaged. Defaults to 25 bp.
  
  -e Integer        The read or feature is extended by the specified distance
                    in bp prior to counting. This option is useful for chip-seq
                    and rna-seq applications. The value is generally set to the
                    average fragment length of the library.
  
  -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>