# HG changeset patch
# User pitagora <ryota.yamanaka@riken.jp>
# Date 1427357542 -32400
# Node ID 424d1dea2823f16306a6e92af51ead493f129ade
# Parent  3aa3807c078fa9b50299232860a7731e122274d6
commit

diff -r 3aa3807c078f -r 424d1dea2823 README.txt
--- a/README.txt	Thu Mar 26 16:29:05 2015 +0900
+++ b/README.txt	Thu Mar 26 17:12:22 2015 +0900
@@ -1,7 +1,7 @@
 This code is originated from the following. Prease refer this for the licence
 information:
 
-matt-shirley's code:
+Matt Shirley's code:
 https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit
 
 If you use this Galaxy tool in work leading to a scientific publication please
diff -r 3aa3807c078f -r 424d1dea2823 fastq_dump.xml
--- a/fastq_dump.xml	Thu Mar 26 16:29:05 2015 +0900
+++ b/fastq_dump.xml	Thu Mar 26 17:12:22 2015 +0900
@@ -112,12 +112,18 @@
     <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
   </stdio>
   <requirements>
-    <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
+    <requirement type="package" version="2.4.5">sratoolkit_centos</requirement>
   </requirements>
   <help>
-    This tool extracts reads from SRA archives using fastq-dump.
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
-    The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
+This code is originated from the following. Prease refer this for the licence
+information:
+
+Matt Shirley's code:
+https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following:
+
+SRA Toolkit: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
   </help>
 </tool>
diff -r 3aa3807c078f -r 424d1dea2823 sam_dump.xml
--- a/sam_dump.xml	Thu Mar 26 16:29:05 2015 +0900
+++ b/sam_dump.xml	Thu Mar 26 17:12:22 2015 +0900
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Extract reads" version="1.1.2">
+<tool id="sam_dump" name="Extract reads" version="2.4.5">
   <description> in SAM format from NCBI SRA.</description>
   <command>
     sam-dump --log-level fatal
@@ -88,12 +88,18 @@
     </data>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
+    <requirement type="package" version="2.4.5">sratoolkit_centos</requirement>
   </requirements>
   <help>
-    This tool extracts reads from sra archives using sam-dump.
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
-    The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
+This code is originated from the following. Prease refer this for the licence
+information:
+
+Matt Shirley's code:
+https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following:
+
+SRA Toolkit: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
   </help>
 </tool>
diff -r 3aa3807c078f -r 424d1dea2823 sra_pileup.xml
--- a/sra_pileup.xml	Thu Mar 26 16:29:05 2015 +0900
+++ b/sra_pileup.xml	Thu Mar 26 17:12:22 2015 +0900
@@ -1,4 +1,4 @@
-<tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
+<tool id="sra_pileup" name="Generate pileup format" version="2.4.5">
   <description> from NCBI sra.</description>
   <command>sra-pileup --log-level fatal 
     #if str( $region ) != "":
@@ -40,12 +40,18 @@
     <data format="pileup" name="output"/>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
+    <requirement type="package" version="2.4.5">sratoolkit_centos</requirement>
   </requirements>
   <help>
-    This tool produces pileup format from sra archives using sra-pileup. 
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
-    The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
+This code is originated from the following. Prease refer this for the licence
+information:
+
+Matt Shirley's code:
+https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following:
+
+SRA Toolkit: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
   </help>
 </tool>
diff -r 3aa3807c078f -r 424d1dea2823 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 26 16:29:05 2015 +0900
+++ b/tool_dependencies.xml	Thu Mar 26 17:12:22 2015 +0900
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sra_toolkit" version="2.4.5">
+  <package name="sratoolkit_centos" version="2.4.5">
     <repository changeset_revision="4e3a12d04e29" name="package_sratoolkit_centos_2_4_5" owner="pitagora" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>