| Previous changeset 25:104499c775e8 (2017-04-13) Next changeset 27:2d4a97506931 (2017-04-13) |
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modified:
GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/tool_dependencies.xml |
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| diff -r 104499c775e8 -r c7bab1a516ce GRsetFromGEO/GRsetFromGEO.xml --- a/GRsetFromGEO/GRsetFromGEO.xml Thu Apr 13 08:31:13 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.xml Thu Apr 13 10:41:44 2017 -0400 |
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| @@ -10,7 +10,7 @@ <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> </inputs> <outputs> - <data format="Rdata" name="output" label="GenomicRatioSet.Rdata"/> + <data format="RData" name="output" label="GenomicRatioSet.Rdata"/> </outputs> <tests> <test> @@ -21,7 +21,7 @@ </collection> </element> </param> - <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/> + <output format="RData" name="output" label="test-data/GenomicRatioSet.Rdata"/> </test> </tests> <help> |
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| diff -r 104499c775e8 -r c7bab1a516ce GRsetFromGEO/tool_dependencies.xml --- a/GRsetFromGEO/tool_dependencies.xml Thu Apr 13 08:31:13 2017 -0400 +++ b/GRsetFromGEO/tool_dependencies.xml Thu Apr 13 10:41:44 2017 -0400 |
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| b'@@ -1,95 +1,276 @@\n <?xml version="1.0"?>\n <tool_dependency>\n- <package name="R" version="3.2.1">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />\n- </package>\n- <install version="1.0">\n- <actions>\n+ <install version="1.0">\n+ <actions>\n <action type="setup_r_environment">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n- <package name="R" version="3.2.1" />\n- </repository>\n- <package>http://bioconductor.org/packages/release/bioc/src/contrib/minfi_1.20.2.tar.gz</package>\n- <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>\n- <package>http://bioconductor.org/packages/release/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>\n- <package>http://bioconductor.org/packages/release/bioc/src/contrib/IRanges_2.4.8.tar.gz</package>\n- <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>\n- <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>\n- <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>\n- <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>\n- <package>https://bioarchive.galaxyproject.org/Biostrings_2.38.0.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/iterators_1.0.8.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.3.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/locfit_1.5-9.1.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/matrixStats_0.14.2.tar.gz</package>\n- <package>https://bioarchive.galaxyproject.org/limma_3.26.0.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/registry_0.3.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/digest_0.6.9.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/stringi_1.0-1.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/magrittr_1.5.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/stringr_1.0.0.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/pkgmaker_0.22.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/rngtools_1.2.4.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/doRNG_1.6.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/DBI_0.3.1.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/RSQLite_1.0.0.tar.gz</package>\n- <package>https://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/bitops_1.0-6.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/RCurl_1.95-4.7.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/XML_3.98-1.3.tar.gz</package>\n- <package>https://depot.galaxyproject.org/package/noarch/lambda.r_1.1.7.tar.gz</package>\n- <package>https://depot.galaxyproject'..b'org/software/reshape/reshape_0.8.6.tar.gz\n+ </package>\n+ <package sha256sum="d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349">\n+ https://depot.galaxyproject.org/software/quadprog/quadprog_1.5-5.tar.gz\n+ </package>\n+ <package sha256sum="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n+ https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n+ </package>\n+ <package sha256sum="bee70645c7cc88250761092762a9d293b4644f311047baecf49fde766d3059bc">\n+ https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz\n+ </package>\n+ <package sha256sum="c6133611cc991dfc17410d06a9ddcc6dcff0153bceffdf7d5a9b7dc42f31afa6">\n+ https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz\n+ </package>\n+ <package sha256sum="cf61732ef9b38ecb6579055d1cd145198ad23a5a9ae4378f94a1494e6c56c884">\n+ https://depot.galaxyproject.org/software/data.table/data.table_1.10.0.tar.gz\n+ </package>\n+ <package sha256sum="d47be4430a1c343c20f9d3f67b8511506904e46be13ea4199769f012f1449209">\n+ https://depot.galaxyproject.org/software/GO.db/GO.db_3.4.0.tar.gz\n+ </package>\n+ <package sha256sum="dfccd4b4d6ec90cd7628fd128d2456d792f406cee4d32b13448dcb0ffe4ab056">\n+ https://depot.galaxyproject.org/software/NMF/NMF_0.20.6.tar.gz\n+ </package>\n+ <package sha256sum="7fa594d9576592e393283ec4fc79fd72128f663bd516e05651957ce1e6fe3c38">\n+ https://depot.galaxyproject.org/software/colorspace/colorspace_1.3-1.tar.gz\n+ </package>\n+ <package sha256sum="31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1">\n+ https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0.tar.gz\n+ </package>\n+ <package sha256sum="7a4957c66ff622d7d1456adfbb728c60d406cdb2a754979797f9dcb0dc8fee99">\n+ https://depot.galaxyproject.org/software/fastmatch/fastmatch_1.0-4.tar.gz\n+ </package>\n+ <package sha256sum="5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1">\n+ https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz\n+ </package>\n+ <package sha256sum="19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f">\n+ https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz\n+ </package>\n+ <package sha256sum="58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430">\n+ https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz\n+ </package>\n+ <package sha256sum="27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9">\n+ https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz\n+ </package>\n+ <package sha256sum="605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f">\n+ https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz\n+ </package>\n+ <package>\n+ https://bioarchive.galaxyproject.org/minfi_1.20.0.tar.gz\n+ </package>\n+ </action>\n+ </actions>\n+ </install>\n+ </tool_dependency>\n' |