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planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
author eschen42
date Mon, 14 Aug 2017 20:57:59 -0400
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b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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1 #!/bin/bash
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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2
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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3 # Constants {{{1
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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4 ################################################################
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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5
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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6 PROG_PATH=$(dirname $0)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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7
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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8 # MAIN {{{1
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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9 ################################################################
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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11 $PROG_PATH/../multivariate_wrapper.R dataMatrix_in $PROG_PATH/../test-data/input-dataMatrix.tsv sampleMetadata_in $PROG_PATH/../test-data/input-sampleMetadata.tsv variableMetadata_in $PROG_PATH/../test-data/input-variableMetadata.tsv respC age predI 1 orthoI 1 testL FALSE sampleMetadata_out $PROG_PATH/outputSampleMetadata.tsv variableMetadata_out $PROG_PATH/outputVariableMetadata.tsv
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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13 # Computed numbers are not always the same. We cannot use diff directly on files.
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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15 # 0) Check they have the same number of lines
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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16 nlines=$(wc -l <"$PROG_PATH/outputSampleMetadata.tsv")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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17 ref_nlines=$(wc -l <"$PROG_PATH/../test-data/output-sampleMetadata.tsv")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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18 if [ $nlines != $ref_nlines ] ; then
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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19 echo "Incorrect output sample metadata." >&2
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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20 exit 1
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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21 fi
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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23 # 1) We check the header line
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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24 head -n 1 "$PROG_PATH/outputSampleMetadata.tsv" > "$PROG_PATH/header.tsv"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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25 head -n 1 "$PROG_PATH/../test-data/output-sampleMetadata.tsv" > "$PROG_PATH/ref_header.tsv"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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26 if ! diff "$PROG_PATH/header.tsv" "$PROG_PATH/ref_header.tsv" ; then
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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27 echo "Incorrect output sample metadata." >&2
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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28 exit 1
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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29 fi
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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31 # 2) We remove computed values and compare what's left
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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32 awk 'BEGIN{FS=OFS="\t"} {$7=$8=$9="";sub("\t\t","\t")}1' "$PROG_PATH/outputSampleMetadata.tsv" > "$PROG_PATH/nocomput.tsv"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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33 awk 'BEGIN{FS=OFS="\t"} {$7=$8=$9="";sub("\t\t","\t")}1' "$PROG_PATH/../test-data/output-sampleMetadata.tsv" > "$PROG_PATH/ref_nocomput.tsv"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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34 if ! diff "$PROG_PATH/nocomput.tsv" "$PROG_PATH/ref_nocomput.tsv" ; then
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
eschen42
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35 echo "Incorrect output sample metadata." >&2
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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36 exit 1
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty
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37 fi