--- a/deepTools_macros.xml	Tue Sep 16 13:46:05 2014 -0400
+++ b/deepTools_macros.xml	Tue Oct 20 14:43:12 2015 -0400
@@ -10,57 +10,67 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
-                    label="Do not extend paired ends"
-                    help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
-
-                <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
-                    label="Ignore duplicates"
-                    help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
-
-                <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
-                    label="Minimum mapping quality"
-                    help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
-
-                <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
-                    label ="Include zeros"
-                    help  ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
-
-                <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
-                    help="If not specified the value is set automatically."/>
-
-                <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
-                    help="If not specified the value is set automatically."/>
-
+                <expand macro="doNotExtendPairedEnds" />
+                <expand macro="ignoreDuplicates" />
+                <expand macro="minMappingQuality" />
+                <expand macro="includeZeros" />
+                <expand macro="zMin_zMax" />
                 <expand macro="colormap" />
             </when>
         </conditional>
     </xml>
 
+
+    <xml name="bigwigCorrelate_mode_actions">
+
+        <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="includeZeros" />
+                <expand macro="zMin_zMax" />
+                <expand macro="colormap" />
+                <expand macro="plotTitle" />
+                <expand macro="plotNumbers" />
+            </when>
+        </conditional>
+    </xml>
+
+
+    <xml name="includeZeros">
+        <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
+            label="Include zeros"
+            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
+    </xml>
+    <xml name="zMin_zMax">
+        <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
+            help="If not specified the value is set automatically. (--zMin)"/>
+        <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
+            help="If not specified the value is set automatically. (--zMax)"/>
+    </xml>
+
     <xml name="region_limit_operation">
         <param name="region" type="text" value=""
             label="Region of the genome to limit the operation to"
-            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
+            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;. (--region)" />
     </xml>
-    
+
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.5.9.1</token>
+    <token name="@WRAPPER_VERSION@">1.5.11</token>
     <xml name="requirements">
         <requirements>
+            <requirement type="package" version="2.7">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
-            <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.9.1">deepTools</requirement>
-            <requirement type="package" version="0.1">ucsc_tools</requirement>
-            <requirement type="package" version="1.7.1">numpy</requirement>
-            <requirement type="package" version="0.7.7">pysam</requirement>
-            <requirement type="package" version="0.12.0">scipy</requirement>
-            <requirement type="package" version="1.2.1">matplotlib</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
-            <requirement type="package" version="12-2013">bx-python</requirement>
+            <requirement type="package" version="1.5.11">deepTools</requirement>
             <yield />
         </requirements>
+        <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
     </xml>
 
@@ -70,7 +80,7 @@
                 label="Did you compute the matrix with more than one groups of regions?"
                 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                 <option value="yes">Yes, I used multiple groups of regions</option>
-                <option value="no">No, I used only one region.</option>
+                <option value="no">No, I used only one group</option>
             </param>
             <when value="no">
                 <conditional name="clustering">
@@ -87,9 +97,9 @@
             </when>
             <when value="yes" />
         </conditional>
+    </xml>
 
-    </xml>
-    <token name="@kmeans_clusterin@">
+    <token name="@KMEANS_CLUSTERING@">
         #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
             #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
                 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
@@ -99,6 +109,51 @@
         #end if
     </token>
 
+    <xml name="samFlag">
+        <param name="samFlag" type="integer" optional="true" value=""
+            label="Filter reads based on the SAM flag"
+            help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
+    </xml>
+    <xml name="plotNumbers">
+        <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 
+            label="Plot the correlation value" 
+            help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
+    </xml>
+    <xml name="doNotExtendPairedEnds">
+        <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
+            label="Do not extend paired ends"
+            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
+    </xml>
+
+    <xml name="ignoreDuplicates">
+        <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
+            label="Ignore duplicates"
+            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
+    </xml>
+
+    <xml name="minMappingQuality">
+        <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
+            label="Minimum mapping quality"
+            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere. (--minMappingQuality)"/>
+    </xml>
+
+    <xml name="skipZeros">
+        <param name="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 might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
+    </xml>
+
+    <xml name="fragmentLength">
+        <param name="fragmentLength" type="integer" value="300" min="1"
+            label="Fragment length used for the sequencing"
+            help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
+    </xml>
+
+    <xml name="scaleFactor">
+        <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
+        <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
+    </xml>
+
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
@@ -109,9 +164,11 @@
             <regex match="Traceback" />
         </stdio>
     </xml>
+
     <xml name="pseudocount">
         <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
     </xml>
+
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -126,11 +183,6 @@
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
 .. _help site: https://github.com/fidelram/deepTools/wiki/
 
-**References**
-
-If you use this Galaxy tool in work leading to a scientific publication please
-cite the following paper:
-
     </token>
     <xml name="citations">
         <citations>
@@ -140,36 +192,46 @@
     </xml>
 
     <xml name="multiple_input_bams">
-        <repeat name="input_files" title="BAM files" min="2">
-            <param name="bamfile" type="data" format="bam" 
-                label="Bam file" 
-                help="The BAM file must be sorted."/>
-            <param name="label" type="text" size="30" optional="true" value=""
-                label="Label"
-                help="Label to use in the output. If not given the dataset name will be used instead."/>
-          </repeat>
+        <param name="bamfiles" type="data" format="bam"
+            label="Bam file" multiple="true"
+            help="The BAM file must be sorted."/>
+    </xml>
+
+    <xml name="multiple_input_bigwigs">
+        <param name="bigwigfiles" type="data" format="bigwig" multiple="True"
+            label="Bigwig file" 
+            help="The Bigwig file must be sorted."/>
+    </xml>
+
+    <xml name="plotTitle">
+        <param name="plotTitle" type="text" value="" size="30" optional="True"
+            label="Title of the plot"
+            help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
     </xml>
 
     <token name="@multiple_input_bams@">
-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+<![CDATA[
         #set files=[]
         #set labels=[]
-        #for $i in $input_files:
-            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
-            #set $temp_input_path = $temp_input_handle.name
-            #silent $temp_input_handle.close()
-            #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
-            #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
-            #silent $files.append('%s.bam' % $temp_input_path)
+        #for $counter, $bamfile in enumerate($bamfiles):
+            ln -s "${bamfile}" "./${counter}.bam" &&
+            ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+            #silent $files.append('%s.bam' % $counter)
+            #silent $labels.append("'%s'" % ($bamfile.display_name))
+        #end for
+]]>
+    </token>
 
-            ##set $files += [str($i.bamfile)]
-            #if str($i.label.value) != "":
-                #set $labels += ["\"%s\"" % ($i.label.value)]
-            #else
-                #set $labels += ["\"%s\"" % ($i.bamfile.name)]
-            #end if
+    <token name="@multiple_input_bigwigs@">
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+        #for $counter, $bigwig in enumerate($bigwigfiles):
+            ln -s "${bigwig}" "${counter}.bw" &&
+            #silent $files.append('%s.bw' % $counter)
+            #silent $labels.append("'%s'" % ($bigwig.display_name))
         #end for
+]]>
     </token>
 
     <xml name="reference_genome_source">
@@ -180,7 +242,7 @@
             </param>
             <when value="cached">
                 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                    <options from_data_table="deepTools_seqs">
+                    <options from_data_table="lastz_seqs">
                         <filter type="sort_by" column="1" />
                         <validator type="no_options" message="No indexes are available." />
                     </options>