root/galaxy-central/tools/evolution/mutate_snp_codon.xml

<tool id="mutate_snp_codon_1" name="Mutate Codons" version="1.0.0">
  <description>with SNPs</description>
  <command interpreter="python">mutate_snp_codon.py $input1 $output1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $codon_seq_col $snp_chrom_col $snp_start_col $snp_end_col $snp_strand_col $snp_observed_col</command>
  <inputs>
    <param name="input1" type="data" format="interval" label="Interval file with joined SNPs" optional="False" help="The interval metadata for this file should be set for the codon positions."/>
    <param name="codon_seq_col" label="Codon Sequence column" type="data_column" data_ref="input1" />
    <param name="snp_chrom_col" label="SNP chromosome column" type="data_column" data_ref="input1" />
    <param name="snp_start_col" label="SNP start column" type="data_column" data_ref="input1" />
    <param name="snp_end_col" label="SNP end column" type="data_column" data_ref="input1" />
    <param name="snp_strand_col" label="SNP strand column" type="data_column" data_ref="input1" />
    <param name="snp_observed_col" label="SNP observed column" type="data_column" data_ref="input1" />
  </inputs>
  <outputs>
    <data name="output1" format="interval" metadata_source="input1"/>
  </outputs>
   <tests>
     <test>
       <param name="input1" value="mutate_snp_codon_in.interval"/>
       <param name="codon_seq_col" value="8"/>
       <param name="snp_chrom_col" value="17"/>
       <param name="snp_start_col" value="18"/>
       <param name="snp_end_col" value="19"/>
       <param name="snp_strand_col" value="22"/>
       <param name="snp_observed_col" value="25"/>
       <output name="output1" file="mutate_snp_codon_out.interval" />
     </test>
   </tests>
  <help>
This tool takes an interval file as input.  This input should contain a set of codon locations and corresponding DNA sequence (such as from the *Extract Genomic DNA* tool) joined to SNP locations with observed values (such as *all fields from selected table* from the snp130 table of hg18 at the UCSC Table browser).  This interval file should have the metadata (chromosome, start, end, strand) set for the columns containing the locations of the codons. The user needs to specify the columns containing the sequence for the codon as well as the genomic positions and observed values (values should be split by '/') for the SNP data as tool input; SNPs positions and sequence substitutes must have a length of exactly 1. Only genomic intervals which yield a different sequence string are output. All sequence characters are converted to uppercase during processing.
  
  For example, using these settings:
  
  * **metadata** **chromosome**, **start**, **end** and **strand** set to **1**, **2**, **3** and **6**, respectively
  * **Codon Sequence column** set to **c8**
  * **SNP chromosome column** set to **c17**
  * **SNP start column** set to **c18**
  * **SNP end column** set to **c19**
  * **SNP strand column** set to **c22**
  * **SNP observed column** set to **c25**
  
  with the following input::
  
    chr1        58995   58998   NM_001005484    0       +       GAA     GAA     Glu     GAA     1177632 28.96   0       2787607 0.422452662804  585     chr1    58996   58997   rs1638318       0       +       A       A       A/G     genomic single  by-submitter    0       0       unknown exact   3
    chr1        59289   59292   NM_001005484    0       +       TTT     TTT     Phe     TTT     714298  17.57   0       1538990 0.464134269878  585     chr1    59290   59291   rs71245814      0       +       T       T       G/T     genomic single  unknown 0       0       unknown exact   3
    chr1        59313   59316   NM_001005484    0       +       AAG     AAG     Lys     AAG     1295568 31.86   0       2289189 0.565950648898  585     chr1    59315   59316   rs2854682       0       -       G       G       C/T     genomic single  by-submitter    0       0       unknown exact   3
    chr1        59373   59376   NM_001005484    0       +       ACA     ACA     Thr     ACA     614523  15.11   0       2162384 0.284187729839  585     chr1    59373   59374   rs2691305       0       -       A       A       C/T     genomic single  unknown 0       0       unknown exact   3
    chr1        59412   59415   NM_001005484    0       +       GCG     GCG     Ala     GCG     299495  7.37    0       2820741 0.106176001271  585     chr1    59414   59415   rs2531266       0       +       G       G       C/G     genomic single  by-submitter    0       0       unknown exact   3
    chr1        59412   59415   NM_001005484    0       +       GCG     GCG     Ala     GCG     299495  7.37    0       2820741 0.106176001271  585     chr1    59414   59415   rs55874132      0       +       G       G       C/G     genomic single  unknown 0       0       coding-synon    exact   1
  
  
  will produce::
  
    chr1        58995   58998   NM_001005484    0       +       GAA     GAA     Glu     GAA     1177632 28.96   0       2787607 0.422452662804  585     chr1    58996   58997   rs1638318       0       +       A       A       A/G     genomic single  by-submitter    0       0       unknown exact   3       GGA
    chr1        59289   59292   NM_001005484    0       +       TTT     TTT     Phe     TTT     714298  17.57   0       1538990 0.464134269878  585     chr1    59290   59291   rs71245814      0       +       T       T       G/T     genomic single  unknown 0       0       unknown exact   3       TGT
    chr1        59313   59316   NM_001005484    0       +       AAG     AAG     Lys     AAG     1295568 31.86   0       2289189 0.565950648898  585     chr1    59315   59316   rs2854682       0       -       G       G       C/T     genomic single  by-submitter    0       0       unknown exact   3       AAA
    chr1        59373   59376   NM_001005484    0       +       ACA     ACA     Thr     ACA     614523  15.11   0       2162384 0.284187729839  585     chr1    59373   59374   rs2691305       0       -       A       A       C/T     genomic single  unknown 0       0       unknown exact   3       GCA
    chr1        59412   59415   NM_001005484    0       +       GCG     GCG     Ala     GCG     299495  7.37    0       2820741 0.106176001271  585     chr1    59414   59415   rs2531266       0       +       G       G       C/G     genomic single  by-submitter    0       0       unknown exact   3       GCC
    chr1        59412   59415   NM_001005484    0       +       GCG     GCG     Ala     GCG     299495  7.37    0       2820741 0.106176001271  585     chr1    59414   59415   rs55874132      0       +       G       G       C/G     genomic single  unknown 0       0       coding-synon    exact   1       GCC
  </help>
</tool>