Mercurial > repos > iuc > stacks2_procrad

diff test-data/gentest.sh @ 0:9993234400f1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:00:33 -0400
parents
children bd5ff77e2036
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.sh	Mon Jul 01 11:00:33 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