--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamCoverage.xml	Mon Jan 25 20:19:01 2016 -0500
@@ -0,0 +1,187 @@
+<tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
+    <description>generates a coverage bigWig file from a given BAM file</description>
+    <macros>
+        <token name="@BINARY@">bamCoverage</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        ln -s '$bamInput' one.bam &&
+        ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
+
+        @BINARY@
+            @THREADS@
+
+            --bam one.bam
+            --outFileName '$outFileName'
+            --outFileFormat '$outFileFormat'
+
+            --binSize $binSize
+
+            #if $scaling.type=='rpkm':
+                --normalizeUsingRPKM
+            #elif $scaling.type=='1x':
+                #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                    --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
+                #else:
+                    --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
+                #end if
+            #elif $scaling.type=='own':
+                --scaleFactor $scaling.scaleFactor
+            #end if
+
+            #if str($region).strip() != '':
+                --region '$region'
+            #end if
+
+            #if $advancedOpt.showAdvancedOpt == "yes":
+                #if $advancedOpt.smoothLength:
+                    --smoothLength '$advancedOpt.smoothLength'
+                #end if
+
+                @ADVANCED_OPTS_READ_PROCESSING@
+                $advancedOpt.skipNAs
+
+                #if str($advancedOpt.ignoreForNormalization).strip() != '':
+                    --ignoreForNormalization $advancedOpt.ignoreForNormalization
+                #end if
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="bamInput" format="bam" type="data" label="BAM file"
+            help="The BAM file must be sorted."/>
+
+        <param name="binSize" type="integer" value="50" min="1"
+            label="Bin size in bases"
+            help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
+
+        <conditional name="scaling">
+            <param name="type" type="select" label="Scaling/Normalization method" >
+                <option value="1x">Normalize coverage to 1x</option>
+                <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
+                <option value="no">Do not normalize or scale</option>
+            </param>
+            <when value="rpkm">
+                <expand macro="scaleFactor" />
+            </when>
+            <when value="no"/>
+            <when value="1x">
+                <expand macro="effectiveGenomeSize" />
+                <expand macro="scaleFactor" />
+            </when>
+        </conditional>
+
+        <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">
+                <expand macro="smoothLength" />
+
+                <param argument="ignoreForNormalization" type="text" value=""
+                    label="Regions that should be excluded for normalization"
+                    help="A list of chromosome names separated by spaces
+                        containing those chromosomes that should be excluded
+                        during normalization. This is useful when
+                        considering samples with unequal coverage across
+                        chromosomes, like male and female samples. Example: chrX chrM" />
+
+                <expand macro="skipNAs" />
+                <expand macro="read_processing_options" />
+
+                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
+                    label="Determine nucleosome positions from MNase-seq data"
+                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />
+
+            </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>
+    <tests>
+        <test>
+            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="showAdvancedOpt" value="no" />
+            <param name="binSize" value="10" />
+            <param name="type" value="no" />
+            <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
+        </test>
+        <test>
+            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="showAdvancedOpt" value="no" />
+            <param name="binSize" value="10" />
+            <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
+        </test>
+        <test>
+            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
+            <param name="outFileFormat" value="bedgraph" />
+            <param name="showAdvancedOpt" value="no" />
+            <param name="binSize" value="10" />
+            <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
+        </test>
+        <test>
+            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="showAdvancedOpt" value="no" />
+            <param name="binSize" value="10" />
+            <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
+        </test>
+        <test>
+            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="outFileFormat" value="bedgraph" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="binSize" value="10" />
+            <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
+read coverages. The way the method works is by first calculating all the
+number of reads (either extended to match the fragment length or not) that
+overlap each bin in the genome. The resulting read counts can be normalized
+using either a given scaling factor, the RPKM formula or to get a 1x depth of
+coverage (RPGC). In the case of paired-end mapping, each read mate is treated
+independently to avoid a bias when a mixture of concordant and discordant
+pairs is present. This means that *each end* will be extended to match the
+fragment length.
+
+.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
+
+
+You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCoverage.html
+
+
+**Output files**:
+
+- coverage file either in bigWig or bedGraph format
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>