Mercurial > repos > iuc > mitos2

comparison gen.sh @ 0:dd589aa77943 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
author iuc
date Fri, 27 Mar 2020 17:53:42 -0400
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-1:000000000000 0:dd589aa77943
1 ## Activate MITOS(1) conda env
2 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=1.0.5 zip
3
4 conda activate mitos1
5
6 tmp=$(mktemp -d)
7 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
8
9 for i in bed faa fas geneorder gff seq
10 do
11 cp $tmp/result.$i test-data/NC_012920.$i
12 done
13 cp $tmp/result test-data/NC_012920.mito
14 cp $tmp/plots/trnA-*.svg test-data/NC_012920_trnA.svg
15 cp $tmp/plots/prot.pdf test-data/NC_012920_prot.pdf
16 cp $tmp/plots/rna.pdf test-data/NC_012920_ncrna.pdf
17 rm -rf $tmp
18
19 conda deactivate
20
21 ## Activate MITOS2 conda env
22 conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=2.0.6 zip
23
24 conda activate mitos2
25
26 # data for 1st test
27 tmp=$(mktemp -d)
28 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
29 cp $tmp/result.bed test-data/mitos2_NC_012920.bed
30 rm -rf $tmp
31
32 # data for 3rd test
33 tmp=$(mktemp -d)
34 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
35 for i in faa fas geneorder gff mitos seq
36 do
37 cp $tmp/result.$i test-data/mitos2_NC_012920.$i
38 done
39 cp $tmp/plots/prot.pdf test-data/mitos2_NC_012920_prot.pdf
40 cp $tmp/plots/rna.pdf test-data/mitos2_NC_012920_ncrna.pdf
41 rm -rf $tmp
42
43 conda deactivate