diff gatk2_macros.xml @ 4:f244b8209eb8 draft

bug fix release

--- a/gatk2_macros.xml	Wed Feb 19 04:39:38 2014 -0500
+++ b/gatk2_macros.xml	Mon Aug 25 17:43:11 2014 -0400
@@ -3,13 +3,16 @@
     <requirements>
       <requirement type="package">gatk2</requirement>
       <requirement type="package" version="0.1.19">samtools</requirement>
+      <requirement type="package" version="1.56.0">picard</requirement>
       <requirement type="set_environment">GATK2_PATH</requirement>
       <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
+      <yield />
     </requirements>
   </xml>
   <token name="@THREADS@">
     --num_threads \${GALAXY_SLOTS:-4}
   </token>
+  <token name="@VERSION@">2.8</token>
   <token name="@JAR_PATH@">
     java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
   </token>
@@ -54,7 +57,7 @@
         #end for
 
         -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
-        
+        -p '--interval_padding "${gatk_param_type.interval_padding}"'
         -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
         #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
             -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
@@ -217,7 +220,9 @@
           <option value="UNION" selected="True">UNION</option>
           <option value="INTERSECTION">INTERSECTION</option>
         </param>
-        
+        <param name="interval_padding" type="integer" value="0" min="0" label="Amount of padding (in bp) to add to each interval"
+            help="This is typically used to add padding around exons when analyzing exomes. (--interval_padding / -ip)"/>
+
         <conditional name="downsampling_type">
           <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
             <option value="NONE" selected="True">NONE</option>
@@ -295,7 +300,7 @@
         <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
 
       </when>
-    </conditional>    
+    </conditional>
   </xml>
   <xml name="analysis_type_conditional">
     <conditional name="analysis_param_type">
@@ -341,4 +346,11 @@
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
   </token>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1038/ng.806</citation>
+      <citation type="doi">10.1101/gr.107524.110</citation>
+      <citation type="doi">10.1002/0471250953.bi1110s43</citation>
+    </citations>
+  </xml>
 </macros>