Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
changeset 14:2d08a1353145 draft default tip
Uploaded
author | davidvanzessen |
---|---|
date | Wed, 04 May 2016 04:06:49 -0400 |
parents | 7eeb7b808af9 |
children | |
files | baseline.xml wrapper.sh |
diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/baseline.xml Tue Mar 22 05:13:24 2016 -0400 +++ b/baseline.xml Wed May 04 04:06:49 2016 -0400 @@ -11,7 +11,7 @@ ${input.id} #end for " - $reference $out_file "$selection" + $reference $out_file "$selection" "$out_table" </command> <inputs> <repeat name="inputs" title="inputs" min="1" default="1"> @@ -55,7 +55,8 @@ </param> </inputs> <outputs> - <data format="pdf" name="out_file" label = "Baseline on ${on_string}"/> + <data format="pdf" name="out_file" label = "Baseline PDF on ${on_string}"/> + <data format="tabular" name="out_table" label = "Baseline Table on ${on_string}"/> </outputs> <help> Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
--- a/wrapper.sh Tue Mar 22 05:13:24 2016 -0400 +++ b/wrapper.sh Wed May 04 04:06:49 2016 -0400 @@ -16,8 +16,11 @@ ref=${10} output=${11} selection=${12} +output_table=${13} outID="result" +echo "$PWD" + echo "testID = $testID" echo "species = $species" echo "substitutionModel = $substitutionModel" @@ -89,8 +92,8 @@ cd $dir Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1 +cp $workdir/result.txt ${output_table} -