# HG changeset patch
# User peterjc
# Date 1505484519 14400
# Node ID 56dede4f07353d3c800efad8f06f8e27f104bbeb
# Parent  ad14a345f1b0d0f2e3061e0558715cc90d4cb636
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65

diff -r ad14a345f1b0 -r 56dede4f0735 tools/mira3/README.rst
--- a/tools/mira3/README.rst	Wed Jun 07 12:33:07 2017 -0400
+++ b/tools/mira3/README.rst	Fri Sep 15 10:08:39 2017 -0400
@@ -10,7 +10,7 @@
 separated file for use in Galaxy).
 
 It is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
 
 
 Automated Installation
@@ -32,7 +32,7 @@
 The suggested location is a new ``tools/mira3`` folder. You will also need to
 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
 the line::
- 
+
   <tool file="mira3/mira.xml" />
 
 If you wish to run the unit tests, also move/copy the ``test-data/`` files
@@ -116,7 +116,7 @@
 
     $ planemo shed_upload --tar_only tools/mira3/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/empty_file.dat
     test-data/tvc_contigs.fasta
     test-data/tvc_mini.fastq
diff -r ad14a345f1b0 -r 56dede4f0735 tools/mira3/mira.xml
--- a/tools/mira3/mira.xml	Wed Jun 07 12:33:07 2017 -0400
+++ b/tools/mira3/mira.xml	Fri Sep 15 10:08:39 2017 -0400
@@ -54,7 +54,7 @@
 ##remove_rollover_tmps, remove_tmp_directory
 -OUT:rrot=1:rtd=1
 
-##put mira temp directory on local storage                                                                              
+##put mira temp directory on local storage
 -DI:trt=/tmp
 
     </command>
@@ -141,7 +141,7 @@
     </outputs>
     <tests>
         <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
-             strain data and miraSearchESTSNPs. Here we just assemble it. --> 
+             strain data and miraSearchESTSNPs. Here we just assemble it. -->
         <test>
             <param name="job_method" value="denovo" />
             <param name="job_type" value="est" />
@@ -150,7 +150,7 @@
             <param name="condSanger|use" value="true" />
             <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
             <param name="condRoche|use" value="false" />
-            <param name="condIllumina|use" value="false" /> 
+            <param name="condIllumina|use" value="false" />
             <param name="condIonTorrent|use" value="false" />
             <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
             <output name="out_qual" file="empty_file.dat" compare="contains" />
@@ -188,7 +188,7 @@
 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
-Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
 
     </help>
     <citations>