# HG changeset patch
# User iuc
# Date 1432061819 14400
# Node ID 3b4172677e2034940f3d4b4f4e19e1e7fdeb48c8

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_ballgown_1_0_3 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09

diff -r 000000000000 -r 3b4172677e20 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 19 14:56:59 2015 -0400
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ballgown" version="1.0.3">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.1.2" />
+                    </repository>
+                    <package>https://depot.galaxyproject.org/package/noarch/BiocGenerics_0.12.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/S4Vectors_0.4.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/IRanges_2.0.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/GenomeInfoDb_1.2.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/XVector_0.6.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/GenomicRanges_1.18.4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/lattice_0.20-30.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/nlme_3.1-120.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/Matrix_1.1-5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/mgcv_1.8-5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/Biobase_2.26.0.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://depot.galaxyproject.org/package/noarch/AnnotationDbi_1.28.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/XML_3.98-1.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/annotate_1.44.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/survival_2.38-1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/genefilter_1.48.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/sva_3.12.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/limma_3.22.6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/zlibbioc_1.12.0.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/Biostrings_2.34.1.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_1.95-4.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/Rsamtools_1.18.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/codetools_0.2-10.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/iterators_1.0.7.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/checkmate_1.5.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/BBmisc_1.9.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/brew_1.0-6.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/digest_0.6.8.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/fail_1.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/base64enc_0.1-2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/sendmailR_1.2-1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/stringr_0.6.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/BatchJobs_1.5.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/BiocParallel_1.0.3.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/GenomicAlignments_1.2.1.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/rtracklayer_1.26.2.tar.gz</package>
+                    <package>https://depot.galaxyproject.org/package/noarch/ballgown_1.0.3.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+[Ballgown](https://github.com/alyssafrazee/ballgown) is a software package designed to facilitate flexible differential expression analysis of RNA-seq data.
+
+Before using the Ballgown R package, a few preprocessing steps are necessary:
+* RNA-seq reads should be aligned to a reference genome. Any junction-aware aligner is appropriate.
+* A transcriptome should be assembled, or a reference transcriptome should be downloaded. Any assembler or download that produces a GTF file denoting the transcriptome's structure is appropriate.
+* Expression for the features in the transcriptome should be estimated. We provide software called _Tablemaker_ that does this estimation. Tablemaker calls _Cufflinks_ version 2.1.1 (&lt;a href="http://dx.doi.org/10.1038/nbt.1621"&gt;Trapnell et al. (2010)&lt;/a&gt;) to estimate transcript-level FPKMs, and provides several alternative expression measurements (e.g. average per-base coverage, number of mapped reads, etc.) for other features. Expression is estimated for each transcript, exon, and intron (junction) in the assembly.
+
+The Ballgown package provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
+
+        </readme>
+    </package>
+</tool_dependency>