--- a/cmeth.xml	Thu Nov 12 12:01:00 2015 +0300
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-<tool id="cmeth" name="Cmeth" version="0.2.0">
-    <description>BS-Seq analysis</description>
-    <requirements>
-        <requirement type="package" version="0.0.1">integration_jar</requirement>
-    </requirements>
-    <stdio>
-        <!-- Wrapper ensures anything other than zero is an error -->
-        <exit_code range="1:"/>
-        <exit_code range=":-1"/>
-    </stdio>
-    <command interpreter="python">
-        #if $action.selection == "analyze"
-            cmeth_wrapper.py "${genome}" "${fdr}" analyze "${bam}"
-        #else
-            cmeth_wrapper.py "${genome}" "${fdr}" compare "${bam1}" "${bam2}"
-        #end if
-    </command>
-    <inputs>
-        <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
-        <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
-        <conditional name="action">
-            <param name="selection" type="select" label="Action">
-                <option value="analyze">Compute methylation</option>
-                <option value="compare">Compare methylation</option>
-            </param>
-            <when value="analyze">
-                <param name="bam" type="data" format="bam" label="Aligned BS-Seq bam" description="BAM BS-Seq Aligned reads to process"/>
-            </when>
-            <when value="compare">
-                <param name="bam1" type="data" format="bam" label="Aligned BS-Seq bam1" description="BAM BS-Seq Aligned reads to process 1"/>
-                <param name="bam2" type="data" format="bam" label="Aligned BS-Seq bam2" description="BAM BS-Seq Aligned reads to process 2"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        #if $action.selection == "analyze"
-        <data name="result" format="csv" label="CG_unmethylated.csv"/>
-        #else
-        <data name="result" format="csv" label="CG_emr.csv"/>
-        #end if
-    </outputs>
-    <help>
-Cmeth is a tool for analyzing and comparing cytosine methylation from WGBS (whole-genome bisulfite sequencing) data.
-Both procedures rely on the nonparametric Bayesian switching HMM.
-https://github.com/JetBrains-Research/cmeth
-    </help>
-</tool>