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author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:27:49 -0600
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<?xml version="1.0"?>

<tool id="hgvs_combine_1" name="Combine multiple HGVS tables">
  <description> to find concordant and discordant variant calls</description>
  <version_string>combine_hgvs_tables -v</version_string>
  <command interpreter="perl">combine_hgvs_tables -q $collapse $output_hgvs_table
       $params.input_hgvs_table_name1 $params.input_hgvs_table1
       $params.input_hgvs_table_name2 $params.input_hgvs_table2
     #if $int($str($params.source_select)) &gt; 2:
       $params.input_hgvs_table_name3 $params.input_hgvs_table3
     #end if
     #if $int($str($params.source_select)) &gt; 3:
       $params.input_hgvs_table_name4 $params.input_hgvs_table4
     #end if
     #if $int($str($params.source_select)) &gt; 4:
       $params.input_hgvs_table_name5 $params.input_hgvs_table5
     #end if
     #if $int($str($params.source_select)) &gt; 5:
       $params.input_hgvs_table_name6 $params.input_hgvs_table6
     #end if
     #if $int($str($params.source_select)) &gt; 6:
       $params.input_hgvs_table_name7 $params.input_hgvs_table7
     #end if
     #if $int($str($params.source_select)) &gt; 7:
       $params.input_hgvs_table_name8 $params.input_hgvs_table8
     #end if
     #if $int($str($params.source_select)) &gt; 8:
       $params.input_hgvs_table_name9 $params.input_hgvs_table9
     #end if
  </command>
  <inputs>
    <param name="collapse" type="boolean" truevalue="true" falsevalue="false" value="False" label="Collapse stats. If unchecked, column values for zygosity, quality, variant and total depth will have multiple values separated by ';'. If checked, each of these columns will be averaged out amongst input values to report a consensus."/>
    <conditional name="params">
      <param name="source_select" type="select" label="Number of variant call tables to combine">
        <option value="2" selected="true">2</option>
        <option value="3">3</option>
        <option value="4">4</option>
        <option value="5">5</option>
        <option value="6">6</option>
        <option value="7">7</option>
        <option value="8">8</option>
        <option value="9">9</option>
      </param>
      <when value="2">
        <param name="input_hgvs_table_name1" type="text" label="Dataset name to be reported in the output (e.g. GATK_calls or Patient001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
      </when>
      <when value="3">
        <param name="input_hgvs_table_name1" type="text" label="Dataset name to be reported in the output (e.g. GATK_calls or Patient001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
      </when>
      <when value="4">
        <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
        <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
        <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
      </when>
      <when value="5">
        <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
        <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
        <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
        <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
        <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
      </when>
      <when value="6">
        <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
        <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
        <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
        <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
        <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
        <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
        <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
      </when>
      <when value="7">
        <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
        <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
        <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
        <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
        <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
        <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
        <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
        <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/>
        <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/>
      </when>
      <when value="8">
        <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
        <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
        <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
        <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
        <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
        <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
        <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
        <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/>
        <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/>
        <param name="input_hgvs_table_name8" type="text" label="Dataset name #8"/>
        <param format="achri_snp_table" name="input_hgvs_table8" type="data" label="Eighth table"/>
      </when>
      <when value="9">
        <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
        <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
        <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
        <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
        <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
        <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
        <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
        <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
        <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
        <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
        <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
        <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
        <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/>
        <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/>
        <param name="input_hgvs_table_name8" type="text" label="Dataset name #8"/>
        <param format="achri_snp_table" name="input_hgvs_table8" type="data" label="Eighth table"/>
        <param name="input_hgvs_table_name9" type="text" label="Dataset name #9"/>
        <param format="achri_snp_table" name="input_hgvs_table9" type="data" label="Nineth table"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="achri_snp_table" name="output_hgvs_table" type="data" label="HGVS variant table, combining multiple call sets"/>
  </outputs>

  <tests>
  </tests>

  <help>
This tool takes multiple annotated HGVS variant tables and outputs a single table with an extra last column describing the list of input tables that reported the variant.
This may be used to combine multiple variant predictions for the same sample (e.g. a frameshift detection tool and a SNP tool, or two SNP tools using different algorithms).
It may also be used to highlight the concordance between individuals with similar phenotypes (common genetic cause), or isolate de novo mutations in a child (where trio data is available).</help>
  

</tool>