# HG changeset patch
# User nturaga
# Date 1461092913 14400
# Node ID 4ed93cb9744fbf72d6817bcab5281701649b2918
# Parent  c83b6496d7e1995ad23cdaf135d467d2b67ce30f
planemo upload for repository https://github.com/nitesh1989/tools-iuc/tree/methylation/tool_collections/methylation_toolkit/minfi commit cd2aa0df28d6d740d86c5aec560f51e74ef3510d-dirty

diff -r c83b6496d7e1 -r 4ed93cb9744f tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 19 14:51:03 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 19 15:08:33 2016 -0400
@@ -28,30 +28,30 @@
                 <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/GenomicRanges_1.22.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/Biostrings_2.38.0.tar.gz</package>
-<!--            <package>https://bioarchive.galaxyproject.org/iterators_1.0.8.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/foreach_1.4.3.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/locfit_1.5-9.1.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/matrixStats_0.14.2.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/locfit_1.5-9.1.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/matrixStats_0.14.2.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/limma_3.26.0.tar.gz</package>
-                <!-- <package>https://bioarchive.galaxyproject.org/registry_0.3.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/digest_0.6.8.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/stringi_0.5-5.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/magrittr_1.5.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/stringr_1.0.0.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/xtable_1.7-4.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/pkgmaker_0.22.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/rngtools_1.2.4.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/doRNG_1.6.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/DBI_0.3.1.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/RSQLite_1.0.0.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/registry_0.3.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/digest_0.6.8.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/stringi_1.0-1.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/doRNG_1.6.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/DBI_0.3.1.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/RSQLite_1.0.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/AnnotationDbi_1.31.17.tar.gz</package>
-                <!-- <package>https://bioarchive.galaxyproject.org/bitops_1.0-6.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/RCurl_1.95-4.7.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/XML_3.98-1.3.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/lambda.r_1.1.7.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/futile.options_1.0.0.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/futile.logger_1.4.1.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/snow_0.3-13.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/RCurl_1.95-4.7.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/XML_3.98-1.3.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/lambda.r_1.1.7.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/futile.options_1.0.0.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/futile.logger_1.4.1.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/snow_0.3-13.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/BiocParallel_1.3.54.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/Rsamtools_1.22.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/GenomicAlignments_1.6.0.tar.gz</package>
@@ -59,21 +59,21 @@
                 <package>https://bioarchive.galaxyproject.org/biomaRt_2.25.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/GenomicFeatures_1.21.13.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/bumphunter_1.10.0.tar.gz</package>
-                <!-- <package>https://bioarchive.galaxyproject.org/beanplot_1.2.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/RColorBrewer_1.1-2.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/nor1mix_1.2-1.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/beanplot_1.2.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/nor1mix_1.2-1.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/multtest_2.25.2.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/siggenes_1.43.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/preprocessCore_1.31.0.tar.gz</package>
-                <!-- <package>https://bioarchive.galaxyproject.org/base64_1.1.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/base64_1.1.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/illuminaio_0.12.0.tar.gz</package>
-                <!-- <package>https://bioarchive.galaxyproject.org/mclust_5.0.2.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/mclust_5.0.2.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/genefilter_1.51.0.tar.gz</package>
-                <!-- <package>https://bioarchive.galaxyproject.org/Rcpp_0.12.1.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/plyr_1.8.3.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/reshape_0.8.5.tar.gz</package> -->
-                <!-- <package>https://bioarchive.galaxyproject.org/quadprog_1.5-5.tar.gz</package> -->
+                <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.1.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/plyr_1.8.3.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/reshape_0.8.5.tar.gz</package>
+                <package>https://cran.r-project.org/src/contrib/quadprog_1.5-5.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/GEOquery_2.35.7.tar.gz</package>
                 <package>https://bioarchive.galaxyproject.org/minfi_1.16.0.tar.gz</package>
             </action>