# HG changeset patch
# User elixir-it
# Date 1568982129 14400
# Node ID 723755ec06be93b5d179ef687cd01965a4ed857d
# Parent  3112ea6b2c5211e69a5b44f3fdf1a4984fc20b97
Uploaded

diff -r 3112ea6b2c52 -r 723755ec06be .shed.yml
--- a/.shed.yml	Thu Oct 25 04:45:32 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-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 3112ea6b2c52 -r 723755ec06be muse_call.xml
--- a/muse_call.xml	Thu Oct 25 04:45:32 2018 -0400
+++ b/muse_call.xml	Fri Sep 20 08:22:09 2019 -0400
@@ -3,6 +3,7 @@
   <requirements>
         <requirement type="package" version="1.0.rc" >muse</requirement>
         <requirement type="package" version="1.7">samtools</requirement>
+        <requirement type="package" version="1.0" >openssl</requirement>
   </requirements>
   <macros>
     <import>muse_macros.xml</import>
@@ -10,7 +11,7 @@
   <command> <![CDATA[
     ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
   
-   	samtools index $input2 2> log && samtools index $input3 2>log && 
+   	samtools index $input2 2> $log && samtools index $input3 2> $log && 
         
         MuSE call -O variant_call
          #if $reference_source.reference_source_selector == "history"
@@ -27,7 +28,9 @@
     #end if
     #if $positions
       -l $positions
-    #end if]]>
+    #end if
+    2> $log  
+    ]]>
   </command>
   <inputs>
     <expand macro="reference_loc"/>
@@ -38,6 +41,7 @@
   </inputs>
   <outputs>
     <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} log"/>
   </outputs>
   <tests>
       <test>
diff -r 3112ea6b2c52 -r 723755ec06be tool-data/muse_index.loc.sample
--- a/tool-data/muse_index.loc.sample	Thu Oct 25 04:45:32 2018 -0400
+++ b/tool-data/muse_index.loc.sample	Fri Sep 20 08:22:09 2019 -0400
@@ -32,7 +32,5 @@
 #is the value stored in the workflow for that parameter. That is why the
 #hg19 entry above looks odd. New genomes can be better-looking.
 #
-hg38	hg38	GRCh38.d1.vd1.fa	/cvmfs/elixir-italy.galaxy.refdata/GRCh38.d1.vd1/GRCh38.d1.vd1.fa
-hg38	hg38	hg38_GATK_bundle	/cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta
-hg19	hg19	hg19_GATK_bundle	/cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/ucsc.hg19/ucsc.hg19.fasta
+#hg19	hg19	hg19_GATK_bundle	/cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/ucsc.hg19/ucsc.hg19.fasta
 
diff -r 3112ea6b2c52 -r 723755ec06be tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Oct 25 04:45:32 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Fri Sep 20 08:22:09 2019 -0400
@@ -2,6 +2,6 @@
     <!-- Locations of indexes in the muse_call mapper format -->
     <table name="muse_index" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/muse_index.loc" />
+        <file path="/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc" />
     </table>
 </tables>