--- a/mapper.xml	Wed Nov 23 16:32:13 2016 -0500
+++ b/mapper.xml	Wed Jul 12 14:38:46 2017 -0400
@@ -1,4 +1,5 @@
 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0">
+    <description>process and map reads to a reference genome</description>
     <macros>
         <macro name="map_params">
             <conditional name="refGenomeSource">
@@ -15,7 +16,7 @@
                     </param>
                 </when> <!-- build-in -->
                 <when value="history">
-                    <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+                    <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />
                 </when> <!-- history -->
             </conditional> <!-- refGenomeSource -->
             <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>
@@ -24,17 +25,17 @@
             </param>
         </macro>
     </macros>
-    <description>
-<![CDATA[
-process and map reads to a reference genome
-]]>
-    </description>
     <requirements>
-        <requirement type="package" version="2.0">mirdeep2_mapper</requirement>
-        <requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
     </requirements>
-
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command>
 <![CDATA[
 
@@ -86,14 +87,6 @@
         -v -n
 ]]>
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <!-- In case the return code has not been set propery check stderr too -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
     <inputs>
         <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>
         <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/>

--- a/tool_dependencies.xml	Wed Nov 23 16:32:13 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="mirdeep2_mapper" version="2.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
-                <action type="move_file">
-                    <source>clip_adapters.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>collapse_reads_md.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>convert_bowtie_output.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>fastaparse.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>fastq2fasta.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>illumina_to_fasta.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>mapper.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>parse_mappings.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>rna2dna.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-
-Processes reads and/or maps them to the reference genome.
-
-input:
-Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used.
-output:
-The output depends on the options used (see below). Either a fasta file with processed reads or an arf file with with mapped reads, or both, are output. 
-
-        </readme>
-    </package>
-</tool_dependency>