--- a/gatk4_Mutect2.xml	Sun May 10 21:57:26 2020 +0000
+++ b/gatk4_Mutect2.xml	Wed May 13 20:20:51 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@2" profile="18.05">
+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@" profile="18.05">
     <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
     <macros>
         <import>macros.xml</import>
@@ -9,8 +9,6 @@
         <![CDATA[
         #include source=$set_sections#
         #include source=$pre_gatk_excl_ints_chth#
-        #include source=$tumor_bam_index_pre_chth#
-        #include source=$normal_bam_index_pre_chth#
         #include source=$pre_gatk_ints_chth#
 
         #set ref_flag='--reference="reference.fa"'
@@ -19,15 +17,25 @@
             ln -s '$reference_source.reference_sequence' reference.fa &&
             samtools faidx reference.fa &&
             gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
-        #else if str($reference_source.reference_source_selector) == 'history'
+        #else if str($reference_source.reference_source_selector) == 'cached'
             ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
             samtools faidx reference.fa &&
             gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
         #else
             #set ref_flag=''
         #end if
-
-        #if str($outputs.output_parameters) == 'yes'
+	
+        #if str($mode.mode_parameters) == 'tumor_only'
+            ln -s $mode.tumor tumor.bam &&
+            ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
+        #else
+            ln -s $mode.tumor tumor.bam &&
+            ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&
+            ln -s $mode.normal normal.bam &&
+            ln -s $mode.normal.metadata.bam_index normal.bam.bai &&
+        #end if
+	
+	#if str($outputs.output_parameters) == 'yes'
             #if str($outputs.debug_assembly) == 'yes'
                 ln -s '$assembly_region_out' assembly-region.tab &&
             #end if
@@ -77,10 +85,10 @@
         gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
 
         #if str($mode.mode_parameters) == 'tumor_only'
-            #include source=$gatk_tumor_bam_input#
+            --input tumor.bam
         #else
-            #include source=$gatk_tumor_bam_input#
-            #include source=$gatk_normal_bam_input#
+            --input tumor.bam
+            --input normal.bam
         #end if
 
         ## OPTIONAL PARAMETERS ##
@@ -286,11 +294,11 @@
                 <option value="somatic">Somatic</option>
             </param>
             <when value="tumor_only">
-                <expand macro="gatk_tumor_bam_req_params"/>
+                <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
             </when>
             <when value="somatic">
-                <expand macro="gatk_tumor_bam_req_params"/>
-                <expand macro="gatk_normal_bam_req_params"/>
+                <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" />
+                <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" />
             </when>
         </conditional>
         <expand macro="gzip_vcf_params"/>
@@ -643,9 +651,10 @@
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
             </conditional>
-            <param name="reference_sequence" ftype="fasta" value="reference.fa" />
+            <param name="reference_sequence" value="hg38"/>
             <param name="gzipped_output" value="false" />
-            <param name="reference_source_selector" value="history" />
+	    <param name="reference_source_selector" value="cached" />
+	    <param name="reference_sequence" value="hg38"/>
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />