Mercurial > repos > davidvanzessen > mutation_analysis
changeset 12:257e98fd3b54 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 30 Mar 2015 05:06:45 -0400 |
| parents | b0242cd1da34 |
| children | d2d80c7d901c |
| files | merge_and_filter.r mutation_analysis.r mutation_analysis.xml tool_dependencies.xml wrapper.sh |
| diffstat | 3 files changed, 30 insertions(+), 3 deletions(-) [+] |
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--- a/mutation_analysis.xml Thu Mar 26 10:16:20 2015 -0400 +++ b/mutation_analysis.xml Mon Mar 30 05:06:45 2015 -0400 @@ -10,6 +10,9 @@ <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> </outputs> <help> - there is no help + Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis. </help> + <requirements> + <requirement type="package" version="0.5.9">bwa</requirement> + </requirements> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Mar 30 05:06:45 2015 -0400 @@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + </set_environment> + + <package name="blastn" version="1.0.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz</action> + <action type="move_file"> + <source>bin/blastn</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable name="BLASTN" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + downloads blast (ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz) and keeps the blastn executable + </readme> + </package> +</tool_dependency> +
--- a/wrapper.sh Thu Mar 26 10:16:20 2015 -0400 +++ b/wrapper.sh Mon Mar 30 05:06:45 2015 -0400 @@ -15,9 +15,9 @@ echo "identification" -python $dir/gene_identification.py --input $PWD/summary.txt --output $PWD/annotatedsummary.txt +python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/annotatedsummary.txt echo "merging" -Rscript $dir/merge_and_filter.r $PWD/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt +Rscript $dir/merge_and_filter.r $outdir/annotatedsummary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/merged.txt $outdir/unmatched.txt genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" echo "R mutation analysis"