diff snpEff_cds_report.xml @ 5:85b933b7d231

Make the reporting of the SnpEff Amino_Acid_change field an option

--- a/snpEff_cds_report.xml	Wed Apr 24 08:00:04 2013 -0500
+++ b/snpEff_cds_report.xml	Fri May 24 08:50:03 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="SnpEff-cds-report" name="SnpEff Ensembl CDS" version="1.1">
+<tool id="SnpEff-cds-report" name="SnpEff Ensembl CDS" version="1.2">
   <description>Report Variant coding sequence changes for SnpEffects</description>
   <command interpreter="python">
    snpEff_cds_report.py --in $snp_effect_vcf 
@@ -16,6 +16,7 @@
    #end if
    $all_effects
    $with_ccds
+   $snpeff_aa_change
    #if $report_format.__str__.find('html') >= 0:
      --html_report $html_report
      --html_dir $html_report.extra_files_path
@@ -136,6 +137,7 @@
     </param>
     <param name="all_effects" type="boolean" truevalue="--all_effects" falsevalue="" checked="false" label="Report the variant coding for each Ensembl Transcript at the variant position" help="Default is to report only the first Transcript that has a cDNA change"/>
     <param name="with_ccds" type="boolean" truevalue="--with_ccds" falsevalue="" checked="false" label="Report the variant coding only for Ensembl Transcripts with a CCDS ID" help=""/>
+    <param name="snpeff_aa_change" type="boolean" truevalue="--snpeff_aa_change" falsevalue="" checked="false" label="Report the Amino_Acid_change from SnpEff" help="Otherwise, report the first changed Animo Acid as: AposA (ref_AA pos_from_Nterminus alt_AA)"/>
     <param name="polya" type="integer" value="5" optional="true" label="Ignore variants that are part of a Poly-A of at least this length" help="Leave blank to turn off poly A filtering">
       <validator type="in_range" message="poly A between 2 and 100 bases" min="2" max="100"/>
     </param>