--- a/deepTools_macros.xml	Mon Feb 05 11:40:26 2018 -0500
+++ b/deepTools_macros.xml	Thu Feb 15 07:05:47 2018 -0500
@@ -1,11 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.5.7</token>
+    <token name="@WRAPPER_VERSION@">3.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.7">deeptools</requirement>
-            <yield />
+            <requirement type="package" version="3.0.0">deeptools</requirement>
+            <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
@@ -100,7 +100,7 @@
     <xml name="includeZeros">
         <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
             label="Include zeros"
-            help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
+            help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />
     </xml>
 
     <xml name="zMin_zMax">
@@ -238,7 +238,7 @@
     <xml name="extendReads">
         <conditional name="doExtendCustom">
             <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
-                help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
+                help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
                      By default *each* read mate is extended.
                      This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
                      Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
@@ -312,7 +312,7 @@
     <xml name="sortRegions">
         <param argument="--sortRegions" type="select" label="Sort regions"
             help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
-            <option value="no">no ordering</option>
+            <option value="no">maintain the same ordering as the input files</option>
             <option value="descend" selected="true">descending order</option>
             <option value="ascend">ascending order</option>
         </param>
@@ -321,19 +321,19 @@
     <xml name="minMappingQuality">
         <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
             label="Minimum mapping quality"
-            help= "If set, only reads with a mapping quality score higher than this value are considered."/>
+            help= "If set, only reads with a mapping quality score at least this high are considered."/>
     </xml>
 
     <xml name="skipZeros">
         <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
             label ="Skip zeros"
-            help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
+            help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />
     </xml>
 
     <xml name="fragmentLength">
-        <param argument="--fragmentLength" type="integer" value="300" min="1"
+        <param argument="--fragmentLength" type="integer" min="1" optional="true"
             label="Fragment length used for the sequencing"
-            help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
+            help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
     </xml>
 
     <xml name="scaleFactor">
@@ -390,13 +390,13 @@
             <option value="Yes">Yes</option>
         </param>
         <when value="No">
-            <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
-                label="Bam file" multiple="true"
+            <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
+                label="BAM/CRAM file" multiple="true"
                 help=""/>
         </when>
         <when value="Yes">
-            <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
-                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
+            <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
+                <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
             </repeat>
         </when>
         </conditional>
@@ -404,7 +404,7 @@
 
     <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
         <conditional name="multibigwig_conditional">
-        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
+        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
 is vital to you, select Yes below.">
             <option value="No" selected="true">No</option>
             <option value="Yes">Yes</option>
@@ -412,11 +412,11 @@
         <when value="No">
             <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
                 label="@LABEL@"
-                help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
+                help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
         </when>
         <when value="Yes">
             <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
-                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
+                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
             </repeat>
         </when>
         </conditional>
@@ -428,6 +428,12 @@
             help="Title of the plot, to be printed on top of the generated image." />
     </xml>
 
+    <xml name="labelRotation">
+        <param argument="--labelRotation" type="integer" value="0"
+            label="Rotation of the X-axis labels (in degrees)"
+            help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
+    </xml>
+
 
     <token name="@multiple_input_bams@">
 <![CDATA[
@@ -438,8 +444,12 @@
             #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                 ln -s "${bamfile}" "./${counter}.bam" &&
-                ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
-                #silent $files.append('%s.bam' % $counter)
+                #if $bamfile.ext == 'bam':
+                    ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
+                #else:
+                    ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
+                #end if
+                #silent $files.append("'%s.bam'" % $counter)
                 #silent $labels.append("'%s'" % identifier)
             #end for
         #else:
@@ -447,7 +457,12 @@
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                 ln -s "${f.bamfiles}" "./${counter}.bam" &&
                 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
-                #silent $files.append('%s.bam' % $counter)
+                #if $f.bamfiles.ext == 'bam':
+                    ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
+                #else:
+                    ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
+                #end if
+                #silent $files.append("'%s.bam'" % $counter)
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
@@ -463,14 +478,14 @@
             #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
-                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
+                #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
-                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
+                #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
@@ -494,7 +509,7 @@
                 --blackListFileName #echo ' '.join($blfiles)#
             #end if
         #end if
-]]> 
+]]>
     </token>
 
     <xml name="multiple_bed">
@@ -515,7 +530,7 @@
             --BED #echo ' '.join($files)#
             --regionLabels #echo ' '.join($labels)#
         #end if
-]]> 
+]]>
     </token>
 
     <xml name="reference_genome_source">
@@ -551,21 +566,27 @@
             <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
                     Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
-                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
+                    We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
                 <option value="93260000">ce10 (93260000)</option>
-                <option value="121400000">dm3 (121400000)</option>
-                <option value="2451960000" selected="true">hg19 (2451960000)</option>
-                <option value="2150570000">mm9 (2150570000)</option>
+                <option value="130428560">dm3 (130428560)</option>
+                <option value="125464728">dm6 (125464728)</option>
+                <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
+                <option value="2701495761">GRCh38/hg38 (2701495761)</option>
+                <option value="2304947926">GRCm37/mm9 (2304947926)</option>
+                <option value="2308125349">GRCm38/mm10 (2308125349)</option>
                 <option value="specific">user specified</option>
             </param>
             <when value="specific">
                 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
-                       help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
+                       help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>
             </when>
-            <when value="2150570000" />
-            <when value="2451960000" />
-            <when value="121400000" />
             <when value="93260000" />
+            <when value="130428560" />
+            <when value="125464728" />
+            <when value="2685511504" />
+            <when value="2701495761" />
+            <when value="2304947926" />
+            <when value="2308125349" />
         </conditional>
     </xml>
 
@@ -596,6 +617,7 @@
             <when value="yes">
                 <yield />
                 <param name="saveSortedRegions" type="boolean"
+                       argument="--outFileSortedRegions"
                        label="Save the regions after skipping zeros or min/max threshold values"
                        help="The order of the regions in the file follows the sorting order selected. This is useful,
                        for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
@@ -605,11 +627,12 @@
 
 
     <xml name="input_image_file_format">
-        <param argument="--outFileFormat" type="select" label="Image file format">
+        <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">
             <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
             <option value="svg">svg</option>
             <option value="eps">eps</option>
+            <option value="plotly">plotly</option>
         </param>
     </xml>
 
@@ -624,6 +647,7 @@
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
                 <when input="output.outFileFormat" value="svg" format="svg" />
                 <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="plotly" format="html" />
             </change_format>
         </data>
     </xml>
@@ -634,6 +658,7 @@
                 <when input="outFileFormat" value="pdf" format="pdf" />
                 <when input="outFileFormat" value="svg" format="svg" />
                 <when input="outFileFormat" value="eps" format="eps" />
+                <when input="outFileFormat" value="plotly" format="html" />
             </change_format>
         </data>
     </xml>
@@ -662,8 +687,7 @@
 
     <xml name="colorMap">
         <param name="colorMap" type="select" label="Color map to use for the heatmap"
-               help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
-               multiple="true">
+               help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>
             <option value="Spectral">Spectral</option>