# HG changeset patch
# User iuc
# Date 1465309564 14400
# Node ID e4a9e0798360e74f14ffe4e41da7c621f1602475
# Parent  692491de7df57db4d3ea0f7e4ab606fe9518207d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 88c982c5adcd32b11d98428fc554a4fdfcc19584

diff -r 692491de7df5 -r e4a9e0798360 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Thu May 12 07:02:10 2016 -0400
+++ b/abundance_estimates_to_matrix.xml	Tue Jun 07 10:26:04 2016 -0400
@@ -200,7 +200,7 @@
     </help>
 
      <citations>
-        <citation type="doi">doi:10.1038/nbt.1883</citation>
+        <citation type="doi">10.1038/nbt.1883</citation>
     </citations>
 </tool>
 
diff -r 692491de7df5 -r e4a9e0798360 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Thu May 12 07:02:10 2016 -0400
+++ b/align_and_estimate_abundance.xml	Tue Jun 07 10:26:04 2016 -0400
@@ -254,7 +254,7 @@
     </help>
 
      <citations>
-        <citation type="doi">doi:10.1038/nbt.1883</citation>
+        <citation type="doi">10.1038/nbt.1883</citation>
     </citations>
 </tool>
 
diff -r 692491de7df5 -r e4a9e0798360 run_DE_analysis.xml
--- a/run_DE_analysis.xml	Thu May 12 07:02:10 2016 -0400
+++ b/run_DE_analysis.xml	Tue Jun 07 10:26:04 2016 -0400
@@ -140,7 +140,7 @@
     </help>
 
      <citations>
-        <citation type="doi">doi:10.1038/nbt.1883</citation>
+        <citation type="doi">10.1038/nbt.1883</citation>
     </citations>
 </tool>
 
diff -r 692491de7df5 -r e4a9e0798360 samples_qccheck.xml
--- a/samples_qccheck.xml	Thu May 12 07:02:10 2016 -0400
+++ b/samples_qccheck.xml	Tue Jun 07 10:26:04 2016 -0400
@@ -108,7 +108,7 @@
     </help>
     
      <citations>
-        <citation type="doi">doi:10.1038/nbt.1883</citation>
+        <citation type="doi">10.1038/nbt.1883</citation>
     </citations>
 </tool>
 
diff -r 692491de7df5 -r e4a9e0798360 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 12 07:02:10 2016 -0400
+++ b/tool_dependencies.xml	Tue Jun 07 10:26:04 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.1.1">
-        <repository changeset_revision="f75117647d9c" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c61a7ad47fb7" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -25,7 +25,7 @@
         <repository changeset_revision="4fa8ed0ffea1" name="package_r_limma_3_28_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
-       <repository changeset_revision="56a98b4043fd" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable>
diff -r 692491de7df5 -r e4a9e0798360 trinity.xml
--- a/trinity.xml	Thu May 12 07:02:10 2016 -0400
+++ b/trinity.xml	Tue Jun 07 10:26:04 2016 -0400
@@ -162,7 +162,7 @@
     </help>
 
      <citations>
-        <citation type="doi">doi:10.1038/nbt.1883</citation>
+        <citation type="doi">10.1038/nbt.1883</citation>
     </citations>
 </tool>