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Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm
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45 changes: 45 additions & 0 deletions
45
gpunit_functionality/version_check/invalid_mix_species1_test.yml
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| # Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| #module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
| module: GSEA | ||
| name: GSEA invalid_mix_species1_test | ||
| description: Test the GSEA version check with files of mixed species no collapsing; expect an error. Note that we need to use remote files to trigger the check. | ||
| params: | ||
| expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_collapsed_symbols.gct" | ||
| gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt", | ||
| "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Mm/m1.all.v2022.1.Mm.symbols.gmt" ] | ||
| number.of.permutations: "10" | ||
| phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" | ||
| target.profile: "" | ||
| permutation.type: "phenotype" | ||
| collapse.dataset: "No_Collapse" | ||
| #chip.platform.file: | ||
| output.file.name: "<expression.dataset_basename>.zip" | ||
| scoring.scheme: "weighted" | ||
| metric.for.ranking.genes: "Signal2Noise" | ||
| gene.list.sorting.mode: "real" | ||
| gene.list.ordering.mode: "descending" | ||
| max.gene.set.size: "500" | ||
| min.gene.set.size: "15" | ||
| collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" | ||
| normalization.mode: "meandiv" | ||
| randomization.mode: "no_balance" | ||
| omit.features.with.no.symbol.match: "true" | ||
| median.for.class.metrics: "false" | ||
| number.of.markers: "100" | ||
| # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
| random.seed: "149" | ||
| create.svgs: "false" | ||
| create.gcts: "false" | ||
| save.random.ranked.lists: "false" | ||
| plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
| make.detailed.gene.set.report: "false" | ||
| selected.gene.sets: "" | ||
| dev.mode: "true" | ||
| alt.delim: "" | ||
| create.zip: "false" | ||
| assertions: | ||
| jobStatus: fail | ||
| files: | ||
| "stderr.txt": | ||
| diffCmd: ../grepMessages.sh | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/invalid_mix_species1_test/stderrMatches.txt" |
47 changes: 47 additions & 0 deletions
47
gpunit_functionality/version_check/invalid_mix_species2_test.yml
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| # Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| #module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
| module: GSEA | ||
| name: GSEA invalid_mix_species2_test | ||
| description: Test the GSEA version check with files of mixed species no collapsing; expect an error. Note that we need to use remote files to trigger the check. | ||
| params: | ||
| expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" | ||
| gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt" ] | ||
| number.of.permutations: "10" | ||
| phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" | ||
| target.profile: "" | ||
| permutation.type: "phenotype" | ||
| collapse.dataset: "Collapse" | ||
| chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/mouse/Human_AFFY_HG_U133_Mouse_Orthologs_MSigDB.v2022.1.Mm.chip" | ||
| # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd | ||
| # to be able to find it, but that makes the code somewhat complicated. | ||
| output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" | ||
| scoring.scheme: "weighted" | ||
| metric.for.ranking.genes: "Signal2Noise" | ||
| gene.list.sorting.mode: "real" | ||
| gene.list.ordering.mode: "descending" | ||
| max.gene.set.size: "500" | ||
| min.gene.set.size: "15" | ||
| collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" | ||
| normalization.mode: "meandiv" | ||
| randomization.mode: "no_balance" | ||
| omit.features.with.no.symbol.match: "true" | ||
| median.for.class.metrics: "false" | ||
| number.of.markers: "100" | ||
| # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
| random.seed: "149" | ||
| create.svgs: "false" | ||
| create.gcts: "false" | ||
| save.random.ranked.lists: "false" | ||
| plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
| make.detailed.gene.set.report: "false" | ||
| selected.gene.sets: "" | ||
| dev.mode: "true" | ||
| alt.delim: "" | ||
| create.zip: "true" | ||
| assertions: | ||
| jobStatus: fail | ||
| files: | ||
| "stderr.txt": | ||
| diffCmd: ../grepMessages.sh | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/invalid_mix_species2_test/stderrMatches.txt" | ||
|
|
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52
gpunit_functionality/version_check/valid_same_vers_with_chip_test.yml
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|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| # Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| #module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
| module: GSEA | ||
| name: GSEA valid_same_vers_with_chip_test | ||
| description: Test the GSEA version check with files of matching version with collapsing. Note that we need to use remote files to trigger the check. | ||
| params: | ||
| expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" | ||
| gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt" ] | ||
| number.of.permutations: "10" | ||
| phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" | ||
| target.profile: "" | ||
| permutation.type: "phenotype" | ||
| collapse.dataset: "Collapse" | ||
| chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v2022.1.Hs.chip" | ||
| # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd | ||
| # to be able to find it, but that makes the code somewhat complicated. | ||
| output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" | ||
| scoring.scheme: "weighted" | ||
| metric.for.ranking.genes: "Signal2Noise" | ||
| gene.list.sorting.mode: "real" | ||
| gene.list.ordering.mode: "descending" | ||
| max.gene.set.size: "500" | ||
| min.gene.set.size: "15" | ||
| collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" | ||
| normalization.mode: "meandiv" | ||
| randomization.mode: "no_balance" | ||
| omit.features.with.no.symbol.match: "true" | ||
| median.for.class.metrics: "false" | ||
| number.of.markers: "100" | ||
| # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
| random.seed: "149" | ||
| create.svgs: "false" | ||
| create.gcts: "false" | ||
| save.random.ranked.lists: "false" | ||
| plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
| make.detailed.gene.set.report: "false" | ||
| selected.gene.sets: "" | ||
| dev.mode: "true" | ||
| alt.delim: "" | ||
| create.zip: "true" | ||
| assertions: | ||
| jobStatus: success | ||
| files: | ||
| "results.edb": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_vers_with_chip_test/results.edb" | ||
| "gene_sets.gmt": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_vers_with_chip_test/gene_sets.gmt" | ||
| "Diabetes_hgu133a_collapsed_to_symbols.rnk": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_vers_with_chip_test/Diabetes_hgu133a_collapsed_to_symbols.rnk" |
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51
gpunit_functionality/version_check/valid_same_version_test.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| # Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| #module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
| module: GSEA | ||
| name: GSEA valid_same_version_test | ||
| description: Test the GSEA version check with files of matching version and no collapsing. Note that we need to use remote files to trigger the check. | ||
| params: | ||
| expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_collapsed_symbols.gct" | ||
| gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt", | ||
| "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ] | ||
| number.of.permutations: "10" | ||
| phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" | ||
| target.profile: "" | ||
| permutation.type: "phenotype" | ||
| collapse.dataset: "No_Collapse" | ||
| #chip.platform.file: | ||
| output.file.name: "<expression.dataset_basename>.zip" | ||
| scoring.scheme: "weighted" | ||
| metric.for.ranking.genes: "Signal2Noise" | ||
| gene.list.sorting.mode: "real" | ||
| gene.list.ordering.mode: "descending" | ||
| max.gene.set.size: "500" | ||
| min.gene.set.size: "15" | ||
| collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" | ||
| normalization.mode: "meandiv" | ||
| randomization.mode: "no_balance" | ||
| omit.features.with.no.symbol.match: "true" | ||
| median.for.class.metrics: "false" | ||
| number.of.markers: "100" | ||
| # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
| random.seed: "149" | ||
| create.svgs: "false" | ||
| create.gcts: "false" | ||
| save.random.ranked.lists: "false" | ||
| plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
| make.detailed.gene.set.report: "false" | ||
| selected.gene.sets: "" | ||
| dev.mode: "true" | ||
| alt.delim: "" | ||
| create.zip: "false" | ||
| assertions: | ||
| jobStatus: success | ||
| files: | ||
| "results.edb": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_version_test/results.edb" | ||
| "gene_sets.gmt": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_version_test/gene_sets.gmt" | ||
| "Diabetes_collapsed_symbols.rnk": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_same_version_test/Diabetes_collapsed_symbols.rnk" |
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57
gpunit_functionality/version_check/valid_warn_mix_vers_with_chip1_test.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| # Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| #module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
| module: GSEA | ||
| name: GSEA valid_warn_mix_vers_with_chip1_test | ||
| description: Test the GSEA version check with files of mixed versions with collapsing; should warn but complete. Note that we need to use remote files to trigger the check. | ||
| params: | ||
| expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a.gct" | ||
| gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.5.1/h.all.v7.5.1.symbols.gmt", | ||
| "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ] | ||
| number.of.permutations: "10" | ||
| phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes.cls" | ||
| target.profile: "" | ||
| permutation.type: "phenotype" | ||
| collapse.dataset: "Collapse" | ||
| chip.platform.file: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v2022.1.Hs.chip" ] | ||
| # Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd | ||
| # to be able to find it, but that makes the code somewhat complicated. | ||
| output.file.name: "Diabetes_hgu133a_collapsed_to_symbols.zip" | ||
| scoring.scheme: "weighted" | ||
| metric.for.ranking.genes: "Signal2Noise" | ||
| gene.list.sorting.mode: "real" | ||
| gene.list.ordering.mode: "descending" | ||
| max.gene.set.size: "500" | ||
| min.gene.set.size: "15" | ||
| collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes" | ||
| normalization.mode: "meandiv" | ||
| randomization.mode: "no_balance" | ||
| omit.features.with.no.symbol.match: "true" | ||
| median.for.class.metrics: "false" | ||
| number.of.markers: "100" | ||
| # Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
| random.seed: "149" | ||
| create.svgs: "false" | ||
| create.gcts: "false" | ||
| save.random.ranked.lists: "false" | ||
| plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
| make.detailed.gene.set.report: "false" | ||
| selected.gene.sets: "" | ||
| dev.mode: "true" | ||
| alt.delim: "" | ||
| create.zip: "true" | ||
| assertions: | ||
| jobStatus: success | ||
| files: | ||
| "results.edb": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip1_test/results.edb" | ||
| "gene_sets.gmt": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip1_test/gene_sets.gmt" | ||
| "Diabetes_hgu133a_collapsed_to_symbols.rnk": | ||
| diffCmd: diff -q --strip-trailing-cr | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/valid_warn_mix_vers_with_chip1_test/Diabetes_hgu133a_collapsed_to_symbols.rnk" | ||
| "stdout.txt": | ||
| diffCmd: ../grepMessages.sh | ||
| diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/version_check/ valid_warn_mix_vers_with_chip1_test/stdoutMatches.txt" | ||
|
|
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