diff mapper.xml @ 3:a8d24f4b6d95 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

--- 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)"/>