# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1356725714 21600
# Node ID 6460f2ba6a60f4607377730b96d56f782078bc13
# Parent  2f9bf8bf42b78ec9d35115f7f4b1937c7fe816d5
Add BQSR and plot_pdf_file options to base_recalibrator.xml

diff -r 2f9bf8bf42b7 -r 6460f2ba6a60 base_recalibrator.xml
--- a/base_recalibrator.xml	Fri Dec 28 12:34:05 2012 -0600
+++ b/base_recalibrator.xml	Fri Dec 28 14:15:14 2012 -0600
@@ -22,6 +22,9 @@
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
+    #if str($input_recal) != 'None':
+        --BQSR "${input_recal}"
+    #end if
     --out "${output_recal}"
     ${standard_covs}
     #if str( $covariates ) != "None":
@@ -29,6 +32,9 @@
             -cov "${cov}"
         #end for
     #end if
+    #if $plot_pdf:
+       --plot_pdf_file $output_pdf
+    #end if
    '
     
     #set $snp_dataset_provided = False
@@ -167,6 +173,12 @@
         </param>
       </when>
     </conditional>
+    <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" >
+      <help>The input covariates table file which enables on-the-fly base quality score recalibration.
+            Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool.
+            Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
+      </help>
+    </param>
     <param name="standard_covs" type="boolean" truevalue="" falsevalue="--no_standard_covs" checked="false" label="Do not use the standard set of covariates in addition to the ones selected" help="--no_standard_covs/-noStandard" />
     <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate &amp;lt;covariate&amp;gt;" >
       <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? -->
@@ -211,7 +223,7 @@
           </when>
         </conditional>
     </repeat>
-    
+    <param name="plot_pdf" type="boolean" truevalue="--plot_pdf_file" falsevalue="" checked="False" label="Output recalibration plots pdf"/>
     <conditional name="gatk_param_type">
       <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
         <option value="basic" selected="True">Basic</option>
@@ -501,6 +513,9 @@
   <outputs>
     <data format="gatk_report" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" />
     <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+    <data format="pdf" name="output_pdf" label="${tool.name} on ${on_string} (plot_pdf_file)">
+      <filter>plot_pdf == True</filter>
+    </data>
   </outputs>
   <tests>
       <test>