# HG changeset patch
# User nturaga
# Date 1461184189 14400
# Node ID a5c03de9ede7b367372713ee087a23036513991f
# Parent  a207166bbeb249ba12ca4997e2557e20a5702d96
planemo upload for repository https://github.com/nitesh1989/tools-iuc/tree/methylation/tool_collections/methylation_toolkit/minfi commit 4f055a2cf9a8ae7e9cc4d7982193c06df8df1fd1-dirty

diff -r a207166bbeb2 -r a5c03de9ede7 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 19 17:23:47 2016 -0400
+++ b/tool_dependencies.xml	Wed Apr 20 16:29:49 2016 -0400
@@ -1,24 +1,21 @@
 <?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" />
-   </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" />
-   </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 name="libcurl" version="7.35">
+        <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="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="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://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz</package>
                     <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
                     <package>http://bioconductor.org/packages/release/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>
@@ -28,30 +25,30 @@
                     <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>
                     <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.22.4.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://depot.galaxyproject.org/package/noarch/iterators_1.0.8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/locfit_1.5-9.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/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://depot.galaxyproject.org/package/noarch/registry_0.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/digest_0.6.9.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/stringi_1.0-1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/magrittr_1.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/stringr_1.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/pkgmaker_0.22.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/rngtools_1.2.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/doRNG_1.6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/DBI_0.3.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/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://depot.galaxyproject.org/package/noarch/bitops_1.0-6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RCurl_1.95-4.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/XML_3.98-1.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/lambda.r_1.1.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/futile.options_1.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/futile.logger_1.4.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/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://bioconductor.org/packages/release/bioc/src/contrib/SummarizedExperiment_1.0.2.tar.gz</package>
@@ -60,46 +57,47 @@
                     <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>https://depot.galaxyproject.org/package/noarch/beanplot_1.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/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>https://depot.galaxyproject.org/package/noarch/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://depot.galaxyproject.org/package/noarch/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://depot.galaxyproject.org/package/noarch/Rcpp_0.12.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/plyr_1.8.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/reshape_0.8.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/quadprog_1.5-5.tar.gz</package>
                     <package>https://bioarchive.galaxyproject.org/GEOquery_2.35.7.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/scales_0.4.0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/rgl_0.95.1441.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/ellipse_0.3-8.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/corpcor_1.6.8.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/cluster_2.0.4.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/irlba_2.0.0.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz</package>
-                    <package>https://cran.r-project.org/src/contrib/mixOmics_5.2.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/colorspace_1.2-6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/dichromat_2.0-0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/labeling_0.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/munsell_0.4.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/reshape2_1.4.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/gtable_0.2.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/scales_0.4.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/ggplot2_2.1.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/rgl_0.95.1441.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/ellipse_0.3-8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/corpcor_1.6.8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/cluster_2.0.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/gridBase_0.4-7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/doParallel_1.0.10.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/NMF_0.20.6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/irlba_2.0.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/igraph_1.0.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/mixOmics_5.2.0.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>
+                    <package>https://depot.galaxyproject.org/package/noarch/getopt_1.20.0.tar.gz</package>
                     <package>https://bioconductor.org/packages/release/data/experiment/src/contrib/FlowSorted.Blood.450k_1.8.0.tar.gz</package>
                 </action>
-         </actions>
-      </install>
-      <readme />
-   </package>
-</tool_dependency>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>
\ No newline at end of file