Mercurial > repos > gandres > vcftools_filter_stats_diversity
comparison VCFToolsStats/vcfToolsStats.sh @ 8:2b6bb9d5e4e9 draft
planemo upload
| author | gandres |
|---|---|
| date | Tue, 12 Apr 2016 05:43:01 -0400 |
| parents | 612066e3f57d |
| children |
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| 7:ca045c1d5fa5 | 8:2b6bb9d5e4e9 |
|---|---|
| 2 | 2 |
| 3 tool_path=$(dirname $0) | 3 tool_path=$(dirname $0) |
| 4 | 4 |
| 5 filein=$1 | 5 filein=$1 |
| 6 fileout_label=$(date "+%Y%m%d%H%M%S") | 6 fileout_label=$(date "+%Y%m%d%H%M%S") |
| 7 fileout_annot=$2 | 7 fileout_het=$2 |
| 8 fileout_het=$3 | 8 fileout_imiss=$3 |
| 9 fileout_imiss=$4 | 9 fileout_sum=$4 |
| 10 fileout_sum=$5 | 10 filelog=$5 |
| 11 filelog=$6 | |
| 12 | 11 |
| 13 | 12 |
| 14 | 13 |
| 15 perl $tool_path/VCFToolsStats.pl --input $filein --out $fileout_label | 14 perl $tool_path/VCFToolsStats.pl --input $filein --out $fileout_label |
| 16 | 15 |
| 17 cp $fileout_label.annotation $fileout_annot ; rm $fileout_label.annotation | |
| 18 cp $fileout_label.het $fileout_het ; rm $fileout_label.het | 16 cp $fileout_label.het $fileout_het ; rm $fileout_label.het |
| 19 cp $fileout_label.imiss $fileout_imiss ; rm $fileout_label.imiss | 17 cp $fileout_label.imiss $fileout_imiss ; rm $fileout_label.imiss |
| 20 cp $fileout_label.TsTv.summary $fileout_sum ; rm $fileout_label.TsTv.summary | 18 cp $fileout_label.TsTv.summary $fileout_sum ; rm $fileout_label.TsTv.summary |
| 21 | 19 |
| 22 cp vcftools.log $filelog | 20 cp vcftools.log $filelog |