# HG changeset patch
# User elixir-it
# Date 1530607573 14400
# Node ID 2ebf2cd4f18fb19fbacf67209dc3407698fb523b
# Parent  5345d2d688d9a71e7f01209bb758f99de26c04df
Uploaded

diff -r 5345d2d688d9 -r 2ebf2cd4f18f mutect2.xml
--- a/mutect2.xml	Mon Jul 02 05:11:23 2018 -0400
+++ b/mutect2.xml	Tue Jul 03 04:46:13 2018 -0400
@@ -19,9 +19,9 @@
       ln -s $input2 normal.bam &&
       ln -s $input1".bai" tumor.bam.bai &&
       ln -s $input2".bai" normal.bam.bai &&
-      #if $reference_source == "history"
-      ln -s $reference genome.fa &&
-      ln -s $reference".fai" genome.fa.fai
+      #if $reference_source.reference_source_selector == "history"
+      ln -s $reference_source.ref_file_h genome.fa &&
+      ln -s $reference_source.ref_file_h".fai" genome.fa.fai &&
       #end if
       #if $list
       ln -s $list position.bed &&
@@ -37,17 +37,18 @@
       #end if
 
       ##TODO creation of .dict file of the genome required by mutect2 to run
-      #if $reference_source == "history"
-      java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log
+      #if $reference_source.reference_source_selector == "history"
+      java -jar \$CONDA_DEFAULT_ENV/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log &&
       #end if
 
       ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it
       ##and move the .jar file to \$CONDA_DEFAULT_ENV/opt/gatk-3.8/ then the mutect2 command is runned
       gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ;
       java -jar \$CONDA_DEFAULT_ENV/opt/gatk-3.8/GenomeAnalysisTK.jar -nct \${GALAXY_SLOTS:-4} -T MuTect2 -I:tumor tumor.bam  -I:normal normal.bam  -o $output
-      #if $reference_source == "history"
+      #if $reference_source.reference_source_selector == "history"
       -R genome.fa
-      #else
+      #end if
+      #if $reference_source.reference_source_selector == "cached"
       -R $reference_source.ref_file.fields.path
       #end if
       ## TODO advanced inputs section if the optional inputs are present their options are added to the command
diff -r 5345d2d688d9 -r 2ebf2cd4f18f mutect2_macros_add_loc.xml
--- a/mutect2_macros_add_loc.xml	Mon Jul 02 05:11:23 2018 -0400
+++ b/mutect2_macros_add_loc.xml	Tue Jul 03 04:46:13 2018 -0400
@@ -15,7 +15,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
+                <param name="ref_file_h" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
             </when> 
       </conditional>
   </macro>