Mercurial > repos > marie-tremblay-metatoul > normalization

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
author workflow4metabolomics
date Tue, 30 Jul 2019 09:43:57 -0400
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221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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1 #!/bin/bash
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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3 # Variables
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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4 script_dir="${0%/*}"
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
parents:
diff changeset
5 normalization_script=$script_dir/galaxy/normalization/NmrNormalization_wrapper.R
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
parents:
diff changeset
6 data_dir=$script_dir/galaxy/normalization/test-data
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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7
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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8 # Run script
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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9 Rscript $normalization_script dataMatrix $data_dir/MTBLS1_bucketedData.tabular scalingMethod Total graphType Overlay logOut norm.log dataMatrixOut $script_dir/matrixout.tabular || exit 1
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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10
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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11 # Test output file
221cbd549c40 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 4bbd4d65e954192aff1a4d210001deb625667136
workflow4metabolomics
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12 diff $data_dir/MTBLS1_bucketedData_normalized.tabular $script_dir/matrixout.tabular || exit 2