# HG changeset patch
# User peterjc
# Date 1496416921 14400
# Node ID 1291ed21789fc0d1ee2176f31983a51cd4cd121f
# Parent  56b421d598059d64ab0dc9ef57c9b05b6bfd00d5
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 1d7d466d01b23d03d214e93f1f8efa19cfa18268

diff -r 56b421d59805 -r 1291ed21789f tools/mira4_0/mira4_de_novo.xml
--- a/tools/mira4_0/mira4_de_novo.xml	Thu May 18 13:36:08 2017 -0400
+++ b/tools/mira4_0/mira4_de_novo.xml	Fri Jun 02 11:22:01 2017 -0400
@@ -131,8 +131,8 @@
             <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)"
                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
-        <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="False" />
-        <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="True" />
+        <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="false" />
+        <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="true" />
     </inputs>
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
diff -r 56b421d59805 -r 1291ed21789f tools/mira4_0/mira4_mapping.xml
--- a/tools/mira4_0/mira4_mapping.xml	Thu May 18 13:36:08 2017 -0400
+++ b/tools/mira4_0/mira4_mapping.xml	Fri Jun 02 11:22:01 2017 -0400
@@ -156,8 +156,8 @@
             <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)"
                    help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
-        <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" />
-        <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" />
+        <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="false" />
+        <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="true" />
     </inputs>
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
diff -r 56b421d59805 -r 1291ed21789f tools/mira4_0/repository_dependencies.xml
--- a/tools/mira4_0/repository_dependencies.xml	Thu May 18 13:36:08 2017 -0400
+++ b/tools/mira4_0/repository_dependencies.xml	Fri Jun 02 11:22:01 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="94e05a9e3957" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="080d217544b0" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 56b421d59805 -r 1291ed21789f tools/mira4_0/tool_dependencies.xml
--- a/tools/mira4_0/tool_dependencies.xml	Thu May 18 13:36:08 2017 -0400
+++ b/tools/mira4_0/tool_dependencies.xml	Fri Jun 02 11:22:01 2017 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="MIRA" version="4.0.2">
-        <repository changeset_revision="c926b5613588" name="package_mira_4_0_2" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b4efe6c4acf7" name="package_mira_4_0_2" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>