Mercurial > repos > iuc > stacks2_shortreads
diff test-data/gentest.sh @ 0:ad7a60726fc3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2019 11:02:39 -0400 |
| parents | |
| children | 43e3eeb2e0ec |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gentest.sh Mon Jul 01 11:02:39 2019 -0400 @@ -0,0 +1,19 @@ +#!/usr/bin/env bash + +mkdir stacks_outputs + +denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && +gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf +rm stacks_outputs/catalog.calls + +mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/ +mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/ +mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/ +mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/ +mv stacks_outputs/tsv2bam.log tsv2bam/ +mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/ +mv stacks_outputs/gstacks.log* gstacks/ +mv stacks_outputs/populations.* populations/ +mv stacks_outputs/denovo_map.log denovo_map/ + +rmdir stacks_outputs