# HG changeset patch
# User peterjc
# Date 1505484554 14400
# Node ID 46d73b942b4354ff8e93727a6a8b818fe4993873
# Parent  259891fce7fd324b4fcfb8f05391f0c30425c446
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65

diff -r 259891fce7fd -r 46d73b942b43 tools/mira4_0/README.rst
--- a/tools/mira4_0/README.rst	Wed Aug 09 13:32:11 2017 -0400
+++ b/tools/mira4_0/README.rst	Fri Sep 15 10:09:14 2017 -0400
@@ -9,7 +9,7 @@
 to where Galaxy expects the files) and associated Galaxy wrapper XML file.
 
 It is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler 
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
 
 It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format,
 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
@@ -38,7 +38,7 @@
 
 First install the 'mira' datatype for Galaxy, available here:
 
-* http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes 
+* http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
 
 There are various Python and XML files to install into Galaxy:
 
@@ -138,7 +138,7 @@
 
     $ planemo shed_upload --tar_only tools/mira4_0/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/U13small_m.fastq
     ...
 
diff -r 259891fce7fd -r 46d73b942b43 tools/mira4_0/mira4_de_novo.xml
--- a/tools/mira4_0/mira4_de_novo.xml	Wed Aug 09 13:32:11 2017 -0400
+++ b/tools/mira4_0/mira4_de_novo.xml	Fri Sep 15 10:09:14 2017 -0400
@@ -38,7 +38,7 @@
 ## point to a local hard drive (not something like NFS on network).
 ## We replace /tmp with an environment variable via mira4.py
 ##
-## -OUT:orc=no is short for -OUTPUT:output_result_caf=no 
+## -OUT:orc=no is short for -OUTPUT:output_result_caf=no
 ## which turns off an output file we don't want anyway.
 
 #for $rg in $read_group
@@ -142,8 +142,8 @@
         <data name="out_maf" format="mira" label="MIRA de novo assembly">
             <filter>maf_wanted is True</filter>
         </data>
-        <!-- TODO?                                                                                                                          
-        <data name="out_contigstats" format="tabular" label="MIRA contig stats" />                                                          
+        <!-- TODO?
+        <data name="out_contigstats" format="tabular" label="MIRA contig stats" />
         -->
         <data name="out_log" format="txt" label="MIRA de novo log" />
     </outputs>
diff -r 259891fce7fd -r 46d73b942b43 tools/mira4_0/repository_dependencies.xml
--- a/tools/mira4_0/repository_dependencies.xml	Wed Aug 09 13:32:11 2017 -0400
+++ b/tools/mira4_0/repository_dependencies.xml	Fri Sep 15 10:09:14 2017 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format).">
-    <repository changeset_revision="f4d34bd3c633" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="34c6c83bf215" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>