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comparison baseline/wrapper.sh @ 98:d714f5ea83d7 draft default tip

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planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents b6f9a640e098
children
comparison
equal deleted inserted replaced
97:fbc6307dd83b 98:d714f5ea83d7
1 #!/bin/bash 1 #!/bin/bash
2
2 dir="$(cd "$(dirname "$0")" && pwd)" 3 dir="$(cd "$(dirname "$0")" && pwd)"
3 4
4 testID=$1 5 testID=$1
5 species=$2 6 species=$2
6 substitutionModel=$3 7 substitutionModel=$3
77 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1 78 #Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region ${inputs[0]} $workdir/ $outID 2>&1
78 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1 79 Rscript --verbose $dir/Baseline_Main.r $testID $species $substitutionModel $mutabilityModel $clonal $fixIndels $region $fasta $workdir/ $outID 2>&1
79 80
80 echo "$workdir/${outID}.txt" 81 echo "$workdir/${outID}.txt"
81 82
82 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '` 83 if [[ -f "$workdir/${outID}.txt" ]]
83 rows=($rows) 84 then
84 #unset rows[${#rows[@]}-1] 85 rows=`tail -n +2 $workdir/${outID}.txt | grep -v "All sequences combined" | grep -n 'Group' | grep -Eoh '^[0-9]+' | tr '\n' ' '`
86 rows=($rows)
87 #unset rows[${#rows[@]}-1]
85 88
86 cd $dir 89 cd $dir
87 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1 90 Rscript --verbose $dir/comparePDFs.r $workdir/${outID}.RData $output ${rows[@]} 2>&1
88 cp $workdir/result.txt ${output_table} 91 cp $workdir/result.txt ${output_table}
92 fi
89 93
90 94
91 95
92