annotate filter_gd_snp.xml @ 22:95a05c1ef5d5

update to devshed revision aaece207bd01

<tool id="gd_filter_gd_snp" name="Filter SNPs" version="1.1.0">
  <description>: Discard some SNPs based on coverage or quality</description>

  <command interpreter="python">
    filter_gd_snp.py "$input" "$p1_input" "$output" "$lo_coverage" "$hi_coverage" "$low_ind_cov" "$lo_quality"
    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
        #set $arg = '%s:%s' % ($individual_col, $individual)
        "$arg"
    #end for
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
    <param name="lo_coverage" type="text" value="0" label="Lower bound on total coverage">
      <sanitizer>
        <valid initial="string.digits">
          <!-- &#37; is the percent (%) character -->
          <add value="&#37;" />
        </valid>
      </sanitizer>
    </param>
    <param name="hi_coverage" type="text" value="1000" label="Upper bound on total coverage">
      <sanitizer>
        <valid initial="string.digits">
          <!-- &#37; is the percent (%) character -->
          <add value="&#37;" />
        </valid>
      </sanitizer>
    </param>
    <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" />
    <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" />
  </inputs>

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

  <tests>
    <test>
      <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
      <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />
      <param name="lo_coverage" value="0" />
      <param name="hi_coverage" value="1000" />
      <param name="low_ind_cov" value="3" />
      <param name="lo_quality" value="30" />
      <output name="output" file="test_out/modify_snp_table/modify.gd_snp" />
    </test>
  </tests>

  <help>

**Dataset formats**

The input datasets are in gd_snp_ and gd_indivs_ formats.
The output dataset is in gd_snp_ format.  (`Dataset missing?`_)

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _gd_indivs: ./static/formatHelp.html#gd_indivs
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

The user specifies that some of the individuals in a gd_snp dataset form a
"population", by supplying a list that has been previously created using the
Specify Individuals tool.  SNPs are then discarded if their total coverage
for the population is too low or too high, or if their coverage or quality
score for any individual in the population is too low.

The upper and lower bounds on total population coverage can be specified
either as read counts or as percentiles (e.g. "5%", with no decimal places).
For percentile bounds the SNPs are ranked by read count, so for example, a
lower bound of "10%" means that the least-covered 10% of the SNPs will be
discarded, while an upper bound of, say, "80%" will discard all SNPs above
the 80% mark, i.e. the top 20%.  The threshold for the lower bound on
individual coverage can only be specified as a plain read count.

-----

**Example**

- input gd_snp::

    Contig161_chr1_4641264_4641879   115  C  T  73.5   chr1   4641382  C   6  0  2  45   8  0  2  51   15  0  2  72   5  0  2  42   6  0  2  45   10  0  2  57   Y  54  0.323  0
    Contig48_chr1_10150253_10151311   11  A  G  94.3   chr1  10150264  A   1  0  2  30   1  0  2  30    1  0  2  30   3  0  2  36   1  0  2  30    1  0  2  30   Y  22  +99.   0
    Contig20_chr1_21313469_21313570   66  C  T  54.0   chr1  21313534  C   4  0  2  39   4  0  2  39    5  0  2  42   4  0  2  39   4  0  2  39    5  0  2  42   N   1  +99.   0
    etc.

- input individuals::

    9   PB1
    13  PB2
    17  PB3

- output when the lower bound on individual coverage is "3"::

    Contig161_chr1_4641264_4641879   115  C  T  73.5   chr1   4641382  C   6  0  2  45   8  0  2  51   15  0  2  72   5  0  2  42   6  0  2  45   10  0  2  57   Y  54  0.323  0
    Contig20_chr1_21313469_21313570   66  C  T  54.0   chr1  21313534  C   4  0  2  39   4  0  2  39    5  0  2  42   4  0  2  39   4  0  2  39    5  0  2  42   N   1  +99.   0
    etc.

  </help>
</tool>