# HG changeset patch
# User fubar
# Date 1420598649 18000
# Node ID 48a6a92bbc308b689c94faf02d02221fdb3f512b
# Parent  635f944c24990d1af660d5ef455e52c8ff0000a2
Uploaded

diff -r 635f944c2499 -r 48a6a92bbc30 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 06 19:36:41 2015 -0500
+++ b/tool_dependencies.xml	Tue Jan 06 21:44:09 2015 -0500
@@ -17,66 +17,65 @@
                     <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="R" version="3.1.2" />
                     </repository>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/stringr_0.6.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtools_3.4.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gdata_2.13.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/bitops_1.0-6.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/caTools_1.17.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/KernSmooth_2.23-13.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gplots_2.15.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.22.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/edgeR_3.8.5.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocGenerics_0.8.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/S4Vectors_0.4.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/IRanges_2.0.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XVector_0.6.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.18.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Biobase_2.26.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/codetools_0.2-9.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/iterators_1.0.7.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreach_1.4.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/checkmate_1.5.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BBmisc_1.8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/brew_1.0-6.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DBI_0.3.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/digest_0.6.8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/fail_1.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RSQLite_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/base64enc_0.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/sendmailR_1.2-1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BatchJobs_1.5.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocParallel_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XML_3.98-1.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/annotate_1.44.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/survival_2.37-7.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.48.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/latticeExtra_0.6-26.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/geneplotter_1.44.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/plyr_1.8.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtable_0.1.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/reshape2_1.4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/dichromat_2.0-0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/colorspace_1.2-4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/munsell_0.4.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/labeling_0.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/scales_0.2.4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/proto_0.3-10.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/MASS_7.3-35.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/ggplot2_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Formula_1.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/cluster_1.15.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rpart_4.1-8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/nnet_7.3-8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/acepack_1.3-3.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreign_0.8-61.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Hmisc_3.14-6.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DESeq2_1.6.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtools_3.4.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gdata_2.13.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/bitops_1.0-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/caTools_1.17.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/KernSmooth_2.23-13.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gplots_2.15.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/limma_3.22.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/codetools_0.2-9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/survival_2.37-7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/MASS_7.3-35.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/cluster_1.15.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/rpart_4.1-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/nnet_7.3-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreign_0.8-61.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true</package>
+
                     
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