--- a/bigwigCompare.xml	Mon Feb 03 13:44:35 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-<tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.3">
-    <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
-    <expand macro="requirements"/>
-    <expand macro="stdio" />
-    <macros>
-        <token name="@BINARY@">bigwigCompare</token>
-        <import>deepTools_macros.xml</import>
-    </macros>
-    <command>
-        bigwigCompare
-
-        @THREADS@
-
-        --bigwig1 '$bigwigFile1'
-        --bigwig2 '$bigwigFile2'
-
-        --outFileName '$outFileName'
-        --outFileFormat '$outFileFormat'
-
-        --ratio $comparison_type
-
-        #if str(region).strip() != '':
-            --region 'region'
-        #end if
-
-        #if $advancedOpt.showAdvancedOpt == "yes":
-
-          --missingDataAsZero $advancedOpt.missingDataAsZero
-          --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
-          --pseudocount '$advancedOpt.pseudocount'
-          --binSize $advancedOpt.binSize
-
-        #end if
-    </command>
-    <inputs>
-        <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
-        <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
-
-        <param name="comparison_type" type="select" 
-                label="How to compare the two files"
-                help="The reciprocal ratio returns the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes." >
-            <option value="log2" selected="true">log2 ratio</option>
-            <option value="ratio">simple ratio</option>
-            <option value="subtract">difference (subtract input from treatment)</option>
-            <option value="add">sum</option>
-            <option value="reciprocal_ratio">reciprocal ratio</option>
-        </param>
-
-        <param name="outFileFormat" type="select" label="Coverage file format">
-            <option value="bigwig" selected="true">bigwig</option>
-            <option value="bedgraph">bedgraph</option>
-        </param>
-
-        <expand macro="region_limit_operation" />
-
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="binSize" type="integer" value="50" min="1" 
-                    label="Bin size in bp"
-                    help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
-
-                <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
-                    label ="Treat missing data as zero"
-                    help  ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
-
-                <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
-                <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
-                <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data format="bigwig" name="outFileName">
-        <change_format>
-            <when input="outFileFormat" value="bigwig" format="bigwig" />
-            <when input="outFileFormat" value="bedgraph" format="bedgraph" />
-        </change_format>
-        </data>
-    </outputs>
-
-  <help>
-
-**What it does**
-
-This tool compares two bigwig files based on the number of mapped reads. To
-compare the bigwig files the genome is partitioned into bins of equal size,
-then the number of reads found in each BAM file are counted for such bins and
-finally a summarizing value is reported. This value can be the ratio of the
-number of reads per bin, the log2 of the ratio, the sum or the difference.
-
-
------
-
-@REFERENCES@
-
-    </help>
-</tool>