Mercurial > repos > davidvanzessen > baseline_bayesian_estimation
changeset 8:525b58fc8622 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 02 Jun 2015 05:02:23 -0400 |
| parents | 45a5e3bd9df4 |
| children | d2b9dd23d944 |
| files | baseline.xml wrapper.sh |
| diffstat | 2 files changed, 9 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/baseline.xml Mon Aug 18 05:54:51 2014 -0400 +++ b/baseline.xml Tue Jun 02 05:02:23 2015 -0400 @@ -46,10 +46,7 @@ <option value="0">Do Nothing</option> <option value="1">Try and fix Indels</option> </param> - <param name="boundaries" type="select" label="FWR/CDR3 Boundaries"> - <option value="1:26:38:55:65:104:-">IMGT® No CDR3</option> - <option value="1:26:38:55:65:104:116">IMGT®</option> - </param> + <param name="boundaries" type="text" value="1:26:38:55:65:104:116" size="40" label="Custom Boundaries (FWR1Start:FWR1End:CDR1End:FWR2End:CDR3End:FWR3End:CDR3End)" /> <param name="selection" type="select" label="Unique Selection Definition"> <option value="VGene,AA.JUNCTION">VGene, AA CDR3</option> <option value="VGene,JGene,AA.JUNCTION">VGene, JGene, AA CDR3</option> @@ -64,6 +61,12 @@ Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27. Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504. + + **Boundaries** + + IMGT® No CDR3: "1:26:38:55:65:104:-" + + IMGT®: "1:26:38:55:65:104:116" </help> </tool>
--- a/wrapper.sh Mon Aug 18 05:54:51 2014 -0400 +++ b/wrapper.sh Tue Jun 02 05:02:23 2015 -0400 @@ -68,6 +68,8 @@ done workdir="$PWD" cd $dir +echo "file: ${inputs[0]}" +#Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 echo "$workdir/${outID}.txt"