Mercurial > repos > elixir-it > muse
changeset 4:3112ea6b2c52 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 25 Oct 2018 04:45:32 -0400 |
| parents | b3152fc222fb |
| children | 723755ec06be |
| files | .shed.yml muse_call.xml |
| diffstat | 2 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- /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
--- 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"/>