diff variant_annotator.xml @ 1:c8752e31f496 draft

Uploaded

--- a/variant_annotator.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_annotator.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,25 +4,23 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #if str( $reference_source.input_bam ) != "None":
-       -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-       #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-           -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-       #end if
-   #end if
-   -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
-   -p '
-   @JAR_PATH@
-    ##--list
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #if str( $reference_source.input_bam ) != "None":
+        -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+        #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+            -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+        #end if
+    #end if
+    -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+    -p '
+    @JAR_PATH@
     -T "VariantAnnotator"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
@@ -92,7 +90,7 @@
       <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
-        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
+        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
@@ -106,9 +104,8 @@
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
-        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files."  help="--intervals"/>
-        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
-        </param>
+        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files."  help="-BTI variant"/>
+        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
@@ -160,7 +157,7 @@
     </repeat>
     
     <conditional name="snpEff_rod_bind_type">
-      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
+      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file (VCF)" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
         <option value="set_snpEff">Set snpEff</option>
         <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
       </param>