Mercurial > repos > yating-l > ucsc_blat

changeset 23:1d17fb76718e draft

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planemo upload commit c6e5cf60eae0c793f7186b7414a0714a14f5c0e7-dirty
author yating-l
date Tue, 23 May 2017 18:27:21 -0400
parents 93159496f9c0
children 4faaa87eca43
files blat.xml tool_dependencies.xml
diffstat 2 files changed, 32 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/blat.xml	Tue May 23 18:21:27 2017 -0400
+++ b/blat.xml	Tue May 23 18:27:21 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0">
+<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
     <description>Standalone blat sequence search command line tool</description>
     <requirements>
-      <requirement type="package" version="35">blat</requirement>
+      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if str($reference_source.reference_source_selector) == "history":
@@ -152,9 +152,9 @@
 http://hgdownload.cse.ucsc.edu/admin/exe/
 
 ]]></help>  
-    <citations>
-        <citation type="doi">10.1101/gr.229202</citation>
-    </citations> 
+<citations>
+      <citation type="doi">10.1101/gr.229202</citation>
+</citations> 
 </tool>
              
             
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 23 18:27:21 2017 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <!-- required tools:
+        - blat
+        - sort
+        - pslReps
+        - faPolyASizes
+        - pslCDnaFilter
+    -->
+    <package name="ucsc_tools_340_for_BLAT" version="1.0">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme>
+    </package>
+</tool_dependency>
\ No newline at end of file