| Previous changeset 63:c3eb6f46884b (2017-06-08) Next changeset 65:ba2b17e5792b (2017-06-08) |
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Commit message:
Uploaded 20170608 |
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modified:
loadandplot.xml plotwithscale.xml testandplot.xml |
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added:
._loadandplot.R ._plotwithscale.R ._testandplot.R test-data/._.DS_Store test-data/input/._Controls_regions.bed test-data/input/._Elements1_regions.bed test-data/input/._Elements2_regions.bed test-data/input/._Elements3_regions.bed test-data/input/._Feature1.bed test-data/input/._Feature2.bed test-data/input/._features.header.bed.txt test-data/input/._regions.header.txt test-data/output_loadandplot/._iwtomics.loadandplot.RData test-data/output_loadandplot/._iwtomics.loadandplot.features.txt test-data/output_loadandplot/._iwtomics.loadandplot.pdf test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.RData test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.tests.txt |
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| diff -r c3eb6f46884b -r bd5ba4648ac0 ._plotwithscale.R |
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| diff -r c3eb6f46884b -r bd5ba4648ac0 ._testandplot.R |
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| diff -r c3eb6f46884b -r bd5ba4648ac0 loadandplot.xml --- a/loadandplot.xml Thu Jun 08 17:12:15 2017 -0400 +++ b/loadandplot.xml Thu Jun 08 17:39:47 2017 -0400 |
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| @@ -5,20 +5,20 @@ </macros> <expand macro="requirements" /> <stdio> - <exit_code range="255" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> - <exit_code range="10" source="both" level="fatal" description="An error has occurred reading the header file for regions. Please try again." /> - <exit_code range="11" source="both" level="fatal" description="Not all region files are present in the first column of header file for regions." /> - <exit_code range="20" source="both" level="fatal" description="An error has occurred reading the header file for features. Please try again." /> - <exit_code range="21" source="both" level="fatal" description="Not all feature files are present in the first column of header file for features." /> - <exit_code range="30" source="both" level="fatal" description="An error has occurred reading the data. Please try again." /> - <exit_code range="31" source="both" level="fatal" description="Not enough columns in input file." /> - <exit_code range="32" source="both" level="fatal" description="Duplicated regions in region file." /> - <exit_code range="33" source="both" level="fatal" description="Duplicated windows in feature file." /> - <exit_code range="34" source="both" level="fatal" description="Overlapping windows in feature file." /> - <exit_code range="35" source="both" level="fatal" description="Windows in feature files do not cover all regions in region files." /> - <exit_code range="36" source="both" level="fatal" description="All windows in a feature file must have the same size." /> - <exit_code range="40" source="both" level="fatal" description="An error has occurred smoothing the data. Please try again." /> - <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." /> + <exit_code range="255" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> + <exit_code range="10" level="fatal" description="An error has occurred reading the header file for regions. Please try again." /> + <exit_code range="11" level="fatal" description="Not all region files are present in the first column of header file for regions." /> + <exit_code range="20" level="fatal" description="An error has occurred reading the header file for features. Please try again." /> + <exit_code range="21" level="fatal" description="Not all feature files are present in the first column of header file for features." /> + <exit_code range="30" level="fatal" description="An error has occurred reading the data. Please try again." /> + <exit_code range="31" level="fatal" description="Not enough columns in input file." /> + <exit_code range="32" level="fatal" description="Duplicated regions in region file." /> + <exit_code range="33" level="fatal" description="Duplicated windows in feature file." /> + <exit_code range="34" level="fatal" description="Overlapping windows in feature file." /> + <exit_code range="35" level="fatal" description="Windows in feature files do not cover all regions in region files." /> + <exit_code range="36" level="fatal" description="All windows in a feature file must have the same size." /> + <exit_code range="40" level="fatal" description="An error has occurred smoothing the data. Please try again." /> + <regex match="Error" level="fatal" description="An error has occurred. Please try again." /> </stdio> <command> |
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| diff -r c3eb6f46884b -r bd5ba4648ac0 plotwithscale.xml --- a/plotwithscale.xml Thu Jun 08 17:12:15 2017 -0400 +++ b/plotwithscale.xml Thu Jun 08 17:39:47 2017 -0400 |
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| @@ -5,14 +5,14 @@ </macros> <expand macro="requirements" /> <stdio> - <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> - <exit_code range="10" source="both" level="fatal" description="Wrong test ids." /> - <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." /> - <exit_code range="30" source="both" level="fatal" description="Two scale thresholds selected for the same test and feature." /> - <exit_code range="40" source="both" level="fatal" description="Scale threshold too high." /> - <exit_code range="50" source="both" level="fatal" description="Group by 'test' but selected features with different resolution." /> - <exit_code range="60" source="both" level="fatal" description="Summary plot error. Please try again." /> - <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." /> + <exit_code range="-1" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> + <exit_code range="10" level="fatal" description="Wrong test ids." /> + <exit_code range="20" level="fatal" description="Wrong feature ids." /> + <exit_code range="30" level="fatal" description="Two scale thresholds selected for the same test and feature." /> + <exit_code range="40" level="fatal" description="Scale threshold too high." /> + <exit_code range="50" level="fatal" description="Group by 'test' but selected features with different resolution." /> + <exit_code range="60" level="fatal" description="Summary plot error. Please try again." /> + <regex match="Error" level="fatal" description="An error has occurred. Please try again." /> </stdio> <command> |
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| diff -r c3eb6f46884b -r bd5ba4648ac0 testandplot.xml --- a/testandplot.xml Thu Jun 08 17:12:15 2017 -0400 +++ b/testandplot.xml Thu Jun 08 17:39:47 2017 -0400 |
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| @@ -5,12 +5,12 @@ </macros> <expand macro="requirements" /> <stdio> - <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> - <exit_code range="10" source="both" level="fatal" description="Wrong region ids." /> - <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." /> - <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." /> - <exit_code range="40" source="both" level="fatal" description="Testing error." /> - <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." /> + <exit_code range="-1" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> + <exit_code range="10" level="fatal" description="Wrong region ids." /> + <exit_code range="20" level="fatal" description="Wrong feature ids." /> + <exit_code range="30" level="fatal" description="Same test repeated multiple times." /> + <exit_code range="40" level="fatal" description="Testing error." /> + <regex match="Error" level="fatal" description="An error has occurred. Please try again." /> </stdio> <command> |