Mercurial > repos > gandres > vcftools_filter_stats_diversity
diff VCFToolFilter/vcfToolsFilter.sh @ 4:b762ecbe2314 draft
planemo upload
| author | gandres |
|---|---|
| date | Fri, 11 Dec 2015 07:35:00 -0500 |
| parents | 612066e3f57d |
| children |
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--- a/VCFToolFilter/vcfToolsFilter.sh Mon Nov 09 05:18:45 2015 -0500 +++ b/VCFToolFilter/vcfToolsFilter.sh Fri Dec 11 07:35:00 2015 -0500 @@ -17,12 +17,12 @@ bound_end=${12} -if [ "${14}" != "None" ] -then samples="--samples ${14}" +if [ "${13}" != "None" ] +then samples="--samples ${13}" fi -if [ "${15}" != "None" ] -then chromosomes="--chromosomes ${15}" +if [ "${14}" != "None" ] +then chromosomes="--chromosomes ${14}" fi if [ "$bound_start" -gt "$bound_end" ] @@ -39,7 +39,7 @@ then cp $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf elif [ "$export" = "freq" ] then cp $fileout_label.frq $fileout ; rm $fileout_label.frq -else cp $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map +else cp $fileout_label.ped $fileout; cp $fileout_label.map ${15} ; rm $fileout_label.ped $fileout_label.map fi cp vcftools.log $filelog