# HG changeset patch
# User nturaga
# Date 1461094118 14400
# Node ID 28a427fb72585c6dc75e20cf102e9ee4b9683e0d
# Parent  4ed93cb9744fbf72d6817bcab5281701649b2918
planemo upload for repository https://github.com/nitesh1989/tools-iuc/tree/methylation/tool_collections/methylation_toolkit/minfi commit cd2aa0df28d6d740d86c5aec560f51e74ef3510d-dirty

diff -r 4ed93cb9744f -r 28a427fb7258 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 19 15:08:33 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 19 15:28:38 2016 -0400
@@ -1,85 +1,83 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="libcurl" version="7.35">
-        <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f8230c44d76c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="http://gaius.bx.psu.edu:8008" />
     </package>
     <package name="R" version="3.2.1">
-        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="r-getopt" version="1.20.0">
-        <repository changeset_revision="712cb82311a8" name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7289a736da57" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="http://gaius.bx.psu.edu:8008" />
     </package>
     <package name="minfi" version="1.16.0">
         <install version="1.0">
-        <actions>
-            <action type="setup_r_environment">
-                <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
-                    <package name="libcurl" version="7.35" />
-                </repository>
-                <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                    <package name="R" version="3.2.1" />
-                </repository>
-                <package>https://bioarchive.galaxyproject.org/BiocGenerics_0.16.0.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/S4Vectors_0.8.0.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/IRanges_2.4.0.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>
-                <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>
-                <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://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://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://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>
-                <package>https://bioarchive.galaxyproject.org/rtracklayer_1.30.0.tar.gz</package>
-                <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://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://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://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://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>
-        </actions>
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="f8230c44d76c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="http://gaius.bx.psu.edu:8008">
+                        <package name="libcurl" version="7.35" />
+                    </repository>
+                    <repository changeset_revision="7289a736da57" name="package_r_3_2_1" owner="iuc" toolshed="http://gaius.bx.psu.edu:8008">
+                        <package name="R" version="3.2.1" />
+                    </repository>
+                    <package>https://bioarchive.galaxyproject.org/BiocGenerics_0.16.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/S4Vectors_0.8.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/IRanges_2.4.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>
+                    <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://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/Archive/matrixStats/matrixStats_0.14.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/limma_3.26.0.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_0.6.9.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/Archive/xtable/xtable_1.7-4.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://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.32.3.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/Archive/RCurl/RCurl_1.95-4.7.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/XML/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/Archive/snow/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>
+                    <package>https://bioarchive.galaxyproject.org/rtracklayer_1.30.0.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/biomaRt_2.26.1.tar.gz</package>
+                    <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicFeatures_1.22.13.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/bumphunter_1.10.0.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>http://bioconductor.org/packages/release/bioc/src/contrib/multtest_2.26.0.tar.gz</package>
+                    <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/siggenes_1.44.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/preprocessCore_1.32.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/base64_1.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/illuminaio_0.12.0.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/mclust/mclust_5.0.2.tar.gz</package>
+                    <package>https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.52.1.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/Archive/Rcpp/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>
+                    <package>https://cran.r-project.org/src/contrib/getopt_1.20.0.tar.gz</package>
+                </action>
+            </actions>
         </install>
-    <readme>
-    </readme>
-</package>
-</tool_dependency>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>
\ No newline at end of file