<tool id="gd_snp2vcf" name="gd_snp to VCF" version="1.0.0" force_history_refresh="True">
  <description>: Convert from gd_snp to VCF format, for submission to dbSNP</description>

  <command interpreter="perl">
    gd_snp2vcf.pl "$input" -handle=$hand -batch=$batch -ref=$ref -metaOut=$output2
    #if $individuals.choice == '0'
      #set $geno = ''
      #for $individual_col in $input.dataset.metadata.individual_columns
        ##need to check to number of cols per individual
        #set $t = $individual_col + 2
        #set $geno += "%d," % ($t)
      #end for
      #if $individuals.pall_id != ''
        -population=$individuals.pall_id
      #end if
    #else if $individuals.choice == '1'
      #set $geno = ''
      #set $pop = ''
      #for $population in $individuals.populations
        -geno=`perl -ane 'print \$F[0]+2, ",";' $population.p1_input`
        #set $pop += "%s," % ($population.p1_id)
      #end for
      -population=$pop
    #else if $individuals.choice == '2'
      #set $geno = $individuals.geno
    #end if
    -geno=$geno
    #if $bioproj.value != ''
       -bioproj=$bioproj
    #end if
    #if $biosamp.value != ''
       -biosamp=$biosamp
    #end if
    > $output
  </command>

  <inputs>
    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
    <conditional name="individuals">
      <param name="choice" type="select" label="Generate dataset for">
        <option value="0" selected="true">All individuals</option>
        <option value="1">Individuals in populations</option>
        <option value="2">A single individual</option>
      </param>
      <when value="0">
        <param name="pall_id" type="text" size="20" label="ID for this population" help="Leaving this blank will omit allele counts from the output" />
      </when>
      <when value="1">
        <repeat name="populations" title="Population" min="1">
        <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" />
        <param name="p1_id" type="text" size="20" label="ID for this population" help="Leaving this blank will omit allele counts from the output" />
        </repeat>
      </when>
      <when value="2">
        <param name="geno" type="data_column" data_ref="input" label="Column containing genotype" value="8" />
      </when>
    </conditional> 
    <param name="hand" type="text" size="20" label="dbSNP handle" help="If you do not have a handle, request one at http://www.ncbi.nlm.nih.gov/projects/SNP/handle.html" />
    <param name="batch" type="text" size="20" label="Batch ID" help="ID used to tie dbSNP metadata to the VCF submission" />
    <param name="ref" type="text" size="20" label="Reference sequence ID" help="The RefSeq assembly accession.version on which the SNP positions are based (see http://www.ncbi.nlm.nih.gov/assembly/)" />
    <param name="bioproj" type="text" size="20" label="Optional: Registered BioProject ID" />
    <param name="biosamp" type="text" size="20" label="Optional: Comma-separated list of registered BioSample IDs" />
  </inputs>

  <outputs>
    <data name="output" format="vcf" />
    <data name="output2" format="text" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="sample.gd_snp" ftype="gd_snp" />
      <param name="choice" value="2" />
      <param name="geno" value="11" />
      <param name="hand" value="MyHandle" />
      <param name="batch" value="Test1" />
      <param name="ref" value="pb_000001.1" />
      <output name="output" file="snpsForSubmission.vcf" ftype="vcf" compare="diff" />
      <output name="output2" file="snpsForSubmission.text" ftype="text" compare="diff" />
    </test>
  </tests>

  <help>

**Dataset formats**

The input dataset is in gd_snp_ format.
The output consists of two datasets needed for submitting SNPs:
a VCF_ file in the specific format required by dbSNP, and a partially
completed text_ file for the associated dbSNP metadata.
(`Dataset missing?`_)

.. _gd_snp: ./static/formatHelp.html#gd_snp
.. _VCF: ./static/formatHelp.html#vcf
.. _text: ./static/formatHelp.html#text
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

This tool converts a dataset in gd_snp format to a VCF file formatted
for submission to the dbSNP database at NCBI.  It also creates a partially
filled-in template to assist you in preparing the required "metadata" file
describing the SNP submission.

-----

**Example**

- input::

    #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",
    #"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}
    Contig161  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   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   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.

- VCF output (for all individuals, and giving a population ID)::

    #CHROM     POS    ID               REF    ALT    QUAL    FILTER  INFO    FORMAT  PB
    Contig161  115    Contig161;115    C      T      73.5    .       VRT=6   NA:AC   8:0
    Contig48   11     Contig48;11      A      G      94.3    .       VRT=6   NA:AC   8:0
    Contig     66     Contig20;66      C      T      54.0    .       VRT=6   NA:AC   8:0
    etc.

Note:  This excerpt from the output does not show all of the headers.  Also,
if the population ID had not been given, then the last two columns would not
appear in the output.

-----

**Reference**

Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K.
dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001
Jan 1;29(1):308-11.

  </help>
</tool>