Mercurial > repos > yusuf > combine_hgvs_annotations

diff CombineHGVSAnnotations.xml @ 0:baf1543e8ae1 default tip

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initial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:27:49 -0600
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CombineHGVSAnnotations.xml	Wed Mar 25 13:27:49 2015 -0600
@@ -0,0 +1,163 @@
+<?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>