# HG changeset patch
# User elixir-it
# Date 1540457132 14400
# Node ID 3112ea6b2c5211e69a5b44f3fdf1a4984fc20b97
# Parent  b3152fc222fbf165a026f2a82c3dbcefb56ce5c7
Uploaded

diff -r b3152fc222fb -r 3112ea6b2c52 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Thu Oct 25 04:45:32 2018 -0400
@@ -0,0 +1,10 @@
+categories:
+- Variant Analysis
+description: 'MuSE:Somatic point mutation caller for tumor-normal paired samples'
+homepage_url: http://bioinformatics.mdanderson.org/main/MuSE
+long_description: |
+MuSE, a novel approach to mutation calling based on the F81 Markov substitution model for molecular evolution, which models the evolution of the reference allele to the allelic composition of the matched tumor and normal tissue at each genomic locus. To improve overall accuracy, we further adopt a sample-specific error model to identify cutoffs, reflecting the variation in tumor heterogeneity among samples. 
+name: muse
+owner: elixir-it
+remote_repository_url: https://github.com/Laniakea-elixir-it/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/MuSE-wrappers
+type: unrestricted
diff -r b3152fc222fb -r 3112ea6b2c52 muse_call.xml
--- a/muse_call.xml	Thu Oct 18 08:17:26 2018 -0400
+++ b/muse_call.xml	Thu Oct 25 04:45:32 2018 -0400
@@ -10,7 +10,7 @@
   <command> <![CDATA[
     ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
   
-   	samtools index $input2 && samtools index $input3 && 
+   	samtools index $input2 2> log && samtools index $input3 2>log && 
         
         MuSE call -O variant_call
          #if $reference_source.reference_source_selector == "history"
@@ -41,7 +41,7 @@
   </outputs>
   <tests>
       <test>
-	<param name="input1" value="test_fasta.fa" ftype="fasta"/>
+        <param name="input1" value="test_fasta.fa" ftype="fasta"/>
         <param name="input2" value="Muse_test_tumoral.bam"/>
         <param name="input3" value="Muse_test_normal.bam"/>
         <output name="output" file="results.txt" lines_diff="8"/>