view igvtools_tile.xml @ 1:ae2bc4e5fefc draft default tip

Fix igvtools_tile.xml tdf output and add log file output

<tool id="igvtools_tile" name="IGVtools tile" version="1.1">
  <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 1> igv.stdout
  </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 ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
    <data format="txt" name="logfile" metadata_source="input" label="${tool.name} on ${on_string}: igv.log" from_work_dir="igv.stdout"/>
  </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>