diff gen.sh @ 0:39b6485e2d34 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
author iuc
date Fri, 27 Mar 2020 17:53:04 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gen.sh	Fri Mar 27 17:53:04 2020 -0400
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+## Activate MITOS(1) conda env
+conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=1.0.5 zip
+
+conda activate mitos1
+
+tmp=$(mktemp -d)
+runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir '/home/maze/workspace/tools-iuc/tools/mitos/test-data/mitos1-refdata/' && zip -9 -y -r $tmp/result.zip $tmp
+
+for i in bed faa fas geneorder gff seq
+do
+	cp $tmp/result.$i test-data/NC_012920.$i
+done
+cp $tmp/result test-data/NC_012920.mito
+cp $tmp/plots/trnA-*.svg test-data/NC_012920_trnA.svg
+cp $tmp/plots/prot.pdf test-data/NC_012920_prot.pdf
+cp $tmp/plots/rna.pdf test-data/NC_012920_ncrna.pdf
+rm -rf $tmp
+
+conda deactivate
+
+## Activate MITOS2 conda env
+conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=2.0.6 zip
+
+conda activate mitos2
+
+# data for 1st test
+tmp=$(mktemp -d)
+runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --finovl 50  --fragovl 0.2 --fragfac 10.0  --evalue 2.0 --cutoff 0.50 --clipfac 10.0     --ncev 0.01  --maxtrnaovl 50 --maxrrnaovl 50  --noplots
+cp $tmp/result.bed test-data/mitos2_NC_012920.bed
+rm -rf $tmp
+
+# data for 3rd test
+tmp=$(mktemp -d)
+runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --evalue 3.0 --cutoff 0.49 --clipfac 9.0 --ncbicode --alarab --oldstst  --ncev 0.1 --sensitive --maxtrnaovl 51 --maxrrnaovl 49 && zip -9 -y -r $tmp/result.zip $tmp
+for i in faa fas geneorder gff mitos seq
+do
+	cp $tmp/result.$i test-data/mitos2_NC_012920.$i
+done
+cp $tmp/plots/prot.pdf test-data/mitos2_NC_012920_prot.pdf
+cp $tmp/plots/rna.pdf test-data/mitos2_NC_012920_ncrna.pdf
+rm -rf $tmp
+
+conda deactivate