update galaxy wrappers to release_1.1

src/galaxy/README.md

@@ -15,5 +15,5 @@ Look at the result and then update the main toolshed.
 
 ## Update toolshed
 
-``planemo shed_update``
+``planemo shed_update --shed_target toolshed``
 

src/galaxy/je-clip.xml

-<tool id="je_clip" name="Je-Clip" version="1.0">
+<tool id="je_clip" name="Je-Clip" version="@VERSION_STRING@">
     <description>clips Unique Molecular Identifiers (UMIs) from fastq files</description>
     <macros>
         <import>macros.xml</import>

src/galaxy/je-demultiplex-illu.xml

-<tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="1.0">
+<tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="@VERSION_STRING@">
     <description>demultiplexes fastq files using Illumina Index file</description>
     <macros>
         <import>macros.xml</import>

src/galaxy/je-demultiplex.xml

-<tool id="je_demultiplex" name="Je-Demultiplex" version="1.0">
+<tool id="je_demultiplex" name="Je-Demultiplex" version="@VERSION_STRING@">
     <description>demultiplexes fastq files</description>
     <macros>
         <import>macros.xml</import>

src/galaxy/je-markdupes.xml

-<tool id="je_markdupes" name="Je-MarkDuplicates" version="1.0">
+<tool id="je_markdupes" name="Je-MarkDuplicates" version="@VERSION_STRING@">
     <description>to filter BAM files for read duplicates taking UMIs into account</description>
     <macros>
         <import>macros.xml</import>

src/galaxy/macros.xml

 <macros>
 
+    <token name="@VERSION_STRING@">1.1</token>
+
     <token name="@single_or_paired_cmd@">
         #if str( $library.type ) == "single":
             F1=${library.input_1}