Mercurial > repos > qfab > rarefaction
comparison rarefaction/rarefactionCurve.sh @ 0:ccdc5e9238fc draft
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| author | qfab |
|---|---|
| date | Sun, 01 Jun 2014 19:46:00 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:ccdc5e9238fc |
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| 1 #!/bin/bash | |
| 2 | |
| 3 echo $@ | |
| 4 | |
| 5 filetype=$1 | |
| 6 input=$2 | |
| 7 pctIdent=$3 | |
| 8 label=0$(bc <<< "scale=2; 1-$pctIdent") | |
| 9 output=$4 | |
| 10 pngOutput=$5 | |
| 11 | |
| 12 ## use Mothur rarefaction.single to calculate rarefaction | |
| 13 mothur "#rarefaction.single($filetype=$input, label=$label)" 2>1 | |
| 14 | |
| 15 ## get filename only remove the extension and copy to galaxy output file | |
| 16 file="${input%.*}" | |
| 17 echo `cp $file.rarefaction $output` |