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annotate test/test-univ @ 1:c00848a8e302 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 6f8da7673d82616b52a7efaf64e4a5ccf0c62bbf
author ethevenot
date Thu, 11 Jan 2018 10:02:02 -0500
parents ab2ee3414e4e
children
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ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
1 #!/bin/bash
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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2
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
3 # Constants {{{1
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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4 ################################################################
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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5
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
6 PROG_PATH=$(dirname $0)
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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7
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
8 # MAIN {{{1
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
9 ################################################################
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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10
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
11 $PROG_PATH/../univariate_wrapper.R dataMatrix_in $PROG_PATH/../test-data/dataMatrix.tsv sampleMetadata_in $PROG_PATH/../test-data/sampleMetadata.tsv variableMetadata_in $PROG_PATH/../test-data/variableMetadata.tsv facC qual tesC kruskal adjC fdr thrN 0.05 variableMetadata_out $PROG_PATH/outputVariableMetadata.tsv
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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12
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
13 if ! diff "$PROG_PATH/outputVariableMetadata.tsv" "$PROG_PATH/../test-data/output-variableMetadata.tsv" ; then
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
diff changeset
14 echo "Incorrect output variable metadata." >&2
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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15 exit 1
ab2ee3414e4e planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 98e8f4464b2f7321acb010e26e2a1c82fe37096e
ethevenot
parents:
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16 fi