<tool id="master2gd_snp" name="MasterVar to gd_snp" version="1.1.0" hidden="false">
  <description>: Convert from MasterVar to gd_snp format</description>
  <command interpreter="perl">
    #if $snptab.tab2 == "yes" 
      #if $snptab.colsOnly.value == "addColsOnly" #master2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly > $out_file1 
      #else #master2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} > $out_file1
      #end if
    #else #master2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} > $out_file1
    #end if
  </command>
  <inputs>
    <param format="tabular" name="input1" type="data" label="Complete Genomics MasterVar dataset" />
    <conditional name="snptab">
      <param name="tab2" type="select" label="Append to gd_snp dataset in history">
        <option value="yes">yes</option>
        <option value="no" selected="true">no</option>
      </param>
      <when value="yes">
      <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" />
      <param name="colsOnly" type="select" label="Skip new SNPs">
        <option value="" selected="true">no</option>
        <option value="addColsOnly">yes</option>
      </param>
      </when>
      <when value="no"> <!-- do nothing -->
      </when>
    </conditional>
    <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" />
  </inputs>
  <outputs>
  <data format="gd_snp" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name='input1' value='masterVarTest.txt' ftype='tab' />
      <param name='tab2' value='no' />
      <param name='indName' value='na' />
      <output name="output" file="master2snp_output.txt" />
    </test>
  </tests>

  <help>

**Dataset formats**

The input dataset is in the MasterVar_ format provided by the Complete Genomics
analysis process (Galaxy considers this to be tabular_, but it must have the
columns specified for MasterVar).
The output dataset is in gd_snp_ format.  (`Dataset missing?`_)

.. _MasterVar: ./static/formatHelp.html#mastervar
.. _tabular: ./static/formatHelp.html#tab
.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

This converts a Complete Genomics MasterVar file to gd_snp format,
so it can be used with the Genome Diversity tools.  It can either
start a new dataset or append to an old one.  When appending, if any new SNPs
appear only in the MasterVar file they can either be skipped or backfilled with
"-1" (unknown) for previous individuals/groups in the gd_snp dataset.
Positions homozygous for the reference allele are skipped.

-----

**Example**

- input MasterVar file::

   934     2       chr1    41980   41981   hom     snp     A       G       G       76      97                      dbsnp.86:rs806721       425     1       1       1       2       -170                            ERVL-E-int:ERVL:47.4    2       1.17    N
   935     2       chr1    41981   42198   hom     ref     =       =       =                                                                                       -170                                            1.17    N
   1102    2       chr1    53205   53206   het-ref snp     G       C       G       93      127                     dbsnp.100:rs2854676     477     7       30      0       37      -127                                    2       1.17    N
   etc.

- output::

   chr1    41980   A       G       -1      0       1       0       76
   chr1    53205   G       C       -1      30      7       1       93
   etc.

</help>
</tool>