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changeset 30:4fa715d44c26 draft

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Uploaded
author david-hoover
date Thu, 20 Sep 2012 10:34:28 -0400
parents 77c0583db74f
children 1326b011a3b9
files print_reads.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/print_reads.xml	Thu Sep 20 10:08:03 2012 -0400
+++ b/print_reads.xml	Thu Sep 20 10:34:28 2012 -0400
@@ -21,7 +21,7 @@
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
-    --recal_file "${input_recal}"
+    --BQSR "${input_recal}"
     --disable_bam_indexing
    '
     ##start standard gatk options
@@ -120,7 +120,7 @@
     #end if
   </command>
   <inputs>
-    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
+    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
         <option value="cached">Locally cached</option>