annotate restore_attributes.xml @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

<tool id="gd_restore_attributes" name="Restore Attributes" version="1.1.0">
  <description>: Fill in missing properties for a gd_snp or gd_genotype dataset</description>

  <command interpreter="python">
    cp.py "$dst" "$output"
  </command>

  <inputs>
    <conditional name="input_type">
      <param name="choice" type="select" format="integer" label="Input format">
        <option value="0" selected="true">gd_snp</option>
        <option value="1">gd_genotype</option>
      </param>

      <when value="0">
        <param name="input" type="data" format="gd_snp" label="SNP dataset to copy attributes from" />
        <param name="dst" type="data" format="gd_snp" label="SNP dataset to receive attributes" />
      </when>
      <when value="1">
        <param name="input" type="data" format="gd_genotype" label="Genotype dataset to copy attributes from" />
        <param name="dst" type="data" format="gd_genotype" label="Genotype dataset to receive attributes" />
      </when>
    </conditional>
  </inputs>

  <outputs>
    <data name="output" format="input" format_source="input" metadata_source="input" />
  </outputs>

  <help>

**Dataset formats**

All of the input and output datasets are in gd_snp_ or gd_genotype_ format.  (`Dataset missing?`_)

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _gd_genotype: ./static/formatHelp.html#gd_genotype
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

This tool copies metadata information from one SNP dataset to another, leaving
the actual SNP data itself unchanged.  Datasets in gd_snp format have a number
of "extra" properties associated with them, such as the focus species (which
may be different from the reference assembly), names of individuals, column
numbers containing certain data fields, etc.  These values are stored in the
dataset's metadata, in addition to the more usual attributes like dataset name,
assembly build, and so forth.  You can see some of these by clicking on the
pencil icon for the dataset.

The Genome Diversity tools need this information to perform their tasks.
However, these additional attributes may be lost if the datatype is changed.
For example, suppose you want to see which SNPs overlap some other dataset in
your history, like coding regions or TAL1 binding sites.  The Intersect tool
only works on datasets that are in interval format, so you might use the Compute
tool to append a new column with the End position of the SNP (= Start + 1),
then use the pencil icon to change the datatype to "interval".  This works
great for doing the intersection, but if you then want to run one of the Genome
Diversity tools on the resulting SNPs, there's a problem: you can change the
datatype back to gd_snp easily enough, but the extra attributes have been lost
in the conversion to interval.

As long as the proper values of the lost attributes have not changed, then this
tool can restore them by copying from the old gd_snp dataset in your history.
In the above example, appending a column does not change the numbering of the
earlier columns, and deleting rows via Intersect does not affect the extra
attributes either.  Note that all of the metadata is copied, not just the extra
attributes specific to gd_snp (though standard items like the assembly build,
the number of lines, and the name for the output dataset are updated
automatically by the Galaxy framework).

  </help>
</tool>