Mercurial > repos > elixir-it > muse
changeset 5:723755ec06be draft
Uploaded
| author | elixir-it |
|---|---|
| date | Fri, 20 Sep 2019 08:22:09 -0400 |
| parents | 3112ea6b2c52 |
| children | b48eb134cfcc |
| files | .shed.yml muse_call.xml tool-data/muse_index.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 8 insertions(+), 16 deletions(-) [+] |
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--- 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
--- 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>
--- 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
--- 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>