changeset 7:602a0c6f4bb0 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:39:03 -0500
parents 8187f841afea
children 2d8543aeeb65
files hicCorrelate.xml involucro macros.xml macros.xml.orig test-data/Li_chrX30-35_cool.png test-data/compare_matrices_log2ratio.h5 test-data/compare_matrices_pearson_ratio.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/diagnostic_plot.png test-data/hicAggregateContacts_results1.png test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicMergeMatrixBins_result1.npz.h5 test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicSumMatrices_result1.npz.h5 test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/master_TADs_plot.png test-data/master_matrix_plot.png test-data/multiFDR_boundaries.bed test-data/multiFDR_boundaries.gff test-data/multiFDR_domains.bed test-data/multiFDR_score.bedgraph test-data/multiFDR_tad_score.bm test-data/multiFDR_zscore_matrix.h5 test-data/obs_exp_small_50kb.cool test-data/obs_exp_small_50kb.h5 test-data/pca1.bedgraph test-data/pca1.bw test-data/pca2.bedgraph test-data/pca2.bw test-data/pearson_small_50kb.cool test-data/pearson_small_50kb.h5 test-data/pearson_small_50kb_transform.cool test-data/raw_qc_report test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_matrix_2.h5 test-data/test_regions.bed
diffstat 40 files changed, 78327 insertions(+), 12493 deletions(-) [+]
line wrap: on
line diff
--- a/hicCorrelate.xml	Tue Jan 02 10:16:20 2018 -0500
+++ b/hicCorrelate.xml	Wed Mar 07 03:39:03 2018 -0500
@@ -18,15 +18,15 @@
             #end if
             $log1p
 
-            #if $use_range.select_use_range == "yes_use_range":
-                --range $range_min:$range_max
-            #end if
+            @USE_RANGE@
 
             #if $chromosomes:
                 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
             #end if
-            
-            --colorMap $colormap
+
+            #if $colormap:
+                --colorMap $colormap
+            #end if
 
             --outFileNameHeatmap ./heatmap.png
             --outFileNameScatter ./scatter.png
@@ -41,25 +41,15 @@
         </param>
         <param name="log1p" type="boolean" argument="--log1p"  truevalue="--log1p" falsevalue=""
             label="Use the log1p of the matrix values" help="(--log1p)" />
-        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
-            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
-                <option value="no_use_range">No restriction</option>
-                <option value="yes_use_range">Only consider counts within a range</option>
-            </param>
-            <when value="no_use_range"/>
-            <when value="yes_use_range">
-                <param name="range_min" type="integer" value="" min="0"/>
-                <param name="range_max" type="integer" value="" min="0"/>
-            </when>
-        </conditional>
+
+        <expand macro="use_range" />
+
         <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
             <param name="chromosome" type="text">
                 <validator type="empty_field" />
             </param>
         </repeat>
-
         <expand macro="colormap" />
-
     </inputs>
     <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
         <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
@@ -90,7 +80,7 @@
                 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
                 <param name="mlabel" value="second"/>
             </repeat>
-            
+
             <param name="log1p" value="True"/>
             <param name="colormap" value="jet"/>
             <param name="method" value="spearman"/>
@@ -116,7 +106,7 @@
 - log scale for the values
 - Correlate full matrix or only specific chromosomes
 - Correlate only within a given range.
-- colormap to use:  Colormap_ 
+- colormap to use:  Colormap_
 
 Output
 ------
Binary file involucro has changed
--- a/macros.xml	Tue Jan 02 10:16:20 2018 -0500
+++ b/macros.xml	Wed Mar 07 03:39:03 2018 -0500
@@ -1,6 +1,13 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">2.0</token>
+    <token name="@WRAPPER_VERSION@">2.1</token>
+
+    <token name="@USE_RANGE@">
+        #if $use_range.select_use_range == "yes_use_range":
+            --range $range_min:$range_max
+        #end if
+    </token>
+
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
@@ -19,6 +26,23 @@
     <xml name="zMax">
         <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
     </xml>
+    <xml name="use_range">
+        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
+            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
+                <option value="no_use_range">No restriction</option>
+                <option value="yes_use_range">Only consider counts within a range</option>
+            </param>
+            <when value="no_use_range"/>
+            <when value="yes_use_range">
+                <expand macro='range' />
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="range">
+        <param name="range_min" type="integer" value="" min="0"/>
+        <param name="range_max" type="integer" value="" min="0"/>
+    </xml>
 
     <xml name="colormap">
         <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
@@ -300,13 +324,12 @@
         <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
     </xml>
     <xml name='matrix_h5_cooler_macro'>
-    <param name='matrix_h5_cooler'  type="data" format="h5,cool" 
-                            label="Matrix to compute on."/>
-       
+        <param name='matrix_h5_cooler' type="data" format="h5,cool"
+            label="Matrix to compute on"/>
     </xml>
     <xml name='matrix_h5_cooler_multiple_macro'>
-        <param name='matrix_h5_cooler_multiple'  type="data" format="h5,cool" 
-                            label="Matrix to compute on." multiple="True"/>
+        <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
+            label="Matricies to compute on" multiple="true"/>
     </xml>
     <token name="@REFERENCES@">
 
@@ -556,9 +579,9 @@
 
     <xml name="spacer_macro">
         <param name="spacer_width" type="float" value="" optional="True"
-                label="Include spacer at the end of the track." help="Width of the spacer." />
+              label="Include spacer at the end of the track." help="Width of the spacer." />
     </xml>
     <xml name="fontsize_macro">
-                    <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+        <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
     </xml>
 </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml.orig	Wed Mar 07 03:39:03 2018 -0500
@@ -0,0 +1,585 @@
+<macros>
+    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
+<<<<<<< HEAD
+    <token name="@WRAPPER_VERSION@">2.0</token>
+
+    <token name="@USE_RANGE@">
+        #if $use_range.select_use_range == "yes_use_range":
+            --range $range_min:$range_max
+        #end if
+    </token>
+
+=======
+    <token name="@WRAPPER_VERSION@">2.1alpha1</token>
+>>>>>>> joachimwolff-master
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
+            <yield />
+        </requirements>
+        <version_command>@BINARY@ --version</version_command>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.1133705</citation>
+            <yield />
+        </citations>
+    </xml>
+
+    <xml name="zMax">
+        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
+    </xml>
+    <xml name="use_range">
+        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
+            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
+                <option value="no_use_range">No restriction</option>
+                <option value="yes_use_range">Only consider counts within a range</option>
+            </param>
+            <when value="no_use_range"/>
+            <when value="yes_use_range">
+                <param name="range_min" type="integer" value="" min="0"/>
+                <param name="range_max" type="integer" value="" min="0"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="colormap">
+        <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
+            <option value="RdYlBu">RdYlBu</option>
+            <option value="Accent">Accent</option>
+            <option value="Spectral">Spectral</option>
+            <option value="Set1">Set1</option>
+            <option value="Set2">Set2</option>
+            <option value="Set3">Set3</option>
+            <option value="Dark2">Dark2</option>
+            <option value="Reds">Reds</option>
+            <option value="Oranges">Oranges</option>
+            <option value="Greens">Greens</option>
+            <option value="Blues">Blues</option>
+            <option value="Greys">Greys</option>
+            <option value="Purples">Purples</option>
+            <option value="Paired">Paired</option>
+            <option value="Pastel1">Pastel1</option>
+            <option value="Pastel2">Pastel2</option>
+            <option value="spring">spring</option>
+            <option value="summer">summer</option>
+            <option value="autumn">autumn</option>
+            <option value="winter">winter</option>
+            <option value="hot">hot</option>
+            <option value="coolwarm">coolwarm</option>
+            <option value="cool">cool</option>
+            <option value="seismic">seismic</option>
+            <option value="terrain">terrain</option>
+            <option value="ocean">ocean</option>
+            <option value="rainbow">rainbow</option>
+            <option value="bone">bone</option>
+            <option value="flag">flag</option>
+            <option value="prism">prism</option>
+            <option value="cubehelix">cubehelix</option>
+            <option value="binary">binary</option>
+            <option value="pink">pink</option>
+            <option value="gray">gray</option>
+            <option value="copper">copper</option>
+            <option value="BrBG">BrBG</option>
+            <option value="BuGn">BuGn</option>
+            <option value="BuPu">BuPu</option>
+            <option value="GnBu">GnBu</option>
+            <option value="OrRd">OrRd</option>
+            <option value="PiYG">PiYG</option>
+            <option value="PRGn">PRGn</option>
+            <option value="PuOr">PuOr</option>
+            <option value="PuRd">PuRd</option>
+            <option value="PuBu">PuBu</option>
+            <option value="RdBu">RdBu</option>
+            <option value="RdGy">RdGy</option>
+            <option value="RdPu">RdPu</option>
+            <option value="YlGn">YlGn</option>
+            <option value="PuBuGn">PuBuGn</option>
+            <option value="RdYlGn">RdYlGn</option>
+            <option value="YlGnBu">YlGnBu</option>
+            <option value="YlOrBr">YlOrBr</option>
+            <option value="YlOrRd">YlOrRd</option>
+            <option value="gist_gray">gist_gray</option>
+            <option value="gist_stern">gist_stern</option>
+            <option value="gist_earth">gist_earth</option>
+            <option value="gist_yarg">gist_yarg</option>
+            <option value="gist_ncar">gist_ncar</option>
+            <option value="gist_rainbow">gist_rainbow</option>
+            <option value="gist_heat">gist_heat</option>
+            <option value="gnuplot">gnuplot</option>
+            <option value="gnuplot2">gnuplot2</option>
+            <option value="CMRmap">CMRmap</option>
+            <option value="bwr">bwr</option>
+            <option value="hsv">hsv</option>
+            <option value="brg">brg</option>
+            <option value="jet">jet</option>
+            <option value="afmhot">afmhot</option>
+            <option value="Accent_r">Accent reversed</option>
+            <option value="Spectral_r">Spectral reversed</option>
+            <option value="Set1_r">Set1 reversed</option>
+            <option value="Set2_r">Set2 reversed</option>
+            <option value="Set3_r">Set3 reversed</option>
+            <option value="Dark2_r">Dark2 reversed</option>
+            <option value="Reds_r">Reds reversed</option>
+            <option value="Oranges_r">Oranges reversed</option>
+            <option value="Greens_r">Greens reversed</option>
+            <option value="Blues_r">Blues reversed</option>
+            <option value="Greys_r">Greys reversed</option>
+            <option value="Purples_r">Purples reversed</option>
+            <option value="Paired_r">Paired reversed</option>
+            <option value="Pastel1_r">Pastel1 reversed</option>
+            <option value="Pastel2_r">Pastel2 reversed</option>
+            <option value="spring_r">spring reversed</option>
+            <option value="summer_r">summer reversed</option>
+            <option value="autumn_r">autumn reversed</option>
+            <option value="winter_r">winter reversed</option>
+            <option value="hot_r">hot reversed</option>
+            <option value="coolwarm_r">coolwarm reversed</option>
+            <option value="cool_r">cool reversed</option>
+            <option value="seismic_r">seismic reversed</option>
+            <option value="terrain_r">terrain reversed</option>
+            <option value="ocean_r">ocean reversed</option>
+            <option value="rainbow_r">rainbow reversed</option>
+            <option value="bone_r">bone reversed</option>
+            <option value="flag_r">flag reversed</option>
+            <option value="prism_r">prism reversed</option>
+            <option value="cubehelix_r">cubehelix reversed</option>
+            <option value="binary_r">binary reversed</option>
+            <option value="pink_r">pink reversed</option>
+            <option value="gray_r">gray reversed</option>
+            <option value="copper_r">copper reversed</option>
+            <option value="BrBG_r">BrBG reversed</option>
+            <option value="BuGn_r">BuGn reversed</option>
+            <option value="BuPu_r">BuPu reversed</option>
+            <option value="GnBu_r">GnBu reversed</option>
+            <option value="OrRd_r">OrRd reversed</option>
+            <option value="PiYG_r">PiYG reversed</option>
+            <option value="PRGn_r">PRGn reversed</option>
+            <option value="PuOr_r">PuOr reversed</option>
+            <option value="PuRd_r">PuRd reversed</option>
+            <option value="PuBu_r">PuBu reversed</option>
+            <option value="RdBu_r">RdBu reversed</option>
+            <option value="RdGy_r">RdGy reversed</option>
+            <option value="RdPu_r">RdPu reversed</option>
+            <option value="YlGn_r">YlGn reversed</option>
+            <option value="PuBuGn_r">PuBuGn reversed</option>
+            <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
+            <option value="RdYlGn_r">RdYlGn reversed</option>
+            <option value="YlGnBu_r">YlGnBu reversed</option>
+            <option value="YlOrBr_r">YlOrBr reversed</option>
+            <option value="YlOrRd_r">YlOrRd reversed</option>
+            <option value="gist_gray_r">gist_gray reversed</option>
+            <option value="gist_stern_r">gist_stern reversed</option>
+            <option value="gist_earth_r">gist_earth reversed</option>
+            <option value="gist_yarg_r">gist_yarg reversed</option>
+            <option value="gist_ncar_r">gist_ncar reversed</option>
+            <option value="gist_rainbow_r">gist_rainbow reversed</option>
+            <option value="gist_heat_r">gist_heat reversed</option>
+            <option value="gnuplot_r">gnuplot reversed</option>
+            <option value="gnuplot2_r">gnuplot2 reversed</option>
+            <option value="CMRmap_r">CMRmap reversed</option>
+            <option value="bwr_r">bwr reversed</option>
+            <option value="hsv_r">hsv reversed</option>
+            <option value="brg_r">brg reversed</option>
+            <option value="jet_r">jet reversed</option>
+            <option value="afmhot_r">afmhot reversed</option>
+        </param>
+    </xml>
+
+
+    <xml name="multiple_input_matrices">
+        <repeat name="input_files" title="HiC Matrix files" min="2">
+            <param name="matrix" type="data" format="h5,cool"
+                label="HiC Matrix file"
+                help=""/>
+            <param name="mlabel" 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>
+    </xml>
+
+    <token name="@multiple_input_matrices@">
+        #set $matrices = []
+        #set $mlabels = []
+        #for $counter, $i in enumerate($input_files):
+            ln -s $i.matrix #echo str($counter)+'_matrix'#;
+            #silent $matrices.append( '%s_matrix' % $counter )
+
+            #if str($i.mlabel.value) != "":
+                #set $mlabels += ['"%s"' % ($i.mlabel.value)]
+            #else
+                #set $mlabels += ['"%s"' % ($i.matrix.name)]
+            #end if
+        #end for
+        #set $mlabels = ' '.join($mlabels)
+        #set $matrices = ' '.join($matrices)
+    </token>
+
+
+    <xml name="region">
+        <param name="region" type="text" label="Region of the genome to limit the operation"
+            help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
+    </xml>
+
+
+
+    <xml name="kmeans_clustering">
+        <conditional name="used_multiple_regions">
+            <param name="used_multiple_regions_options" type="select"
+                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 group</option>
+            </param>
+            <when value="no">
+                <conditional name="clustering">
+                    <param name="clustering_options" type="select" label="Clustering algorithm">
+                        <option value="none">No clustering</option>
+                        <option value="kmeans">Kmeans clustering</option>
+                    </param>
+                    <when value="kmeans">
+                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
+                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
+                    </when>
+                    <when value="none" />
+                </conditional>
+            </when>
+            <when value="yes" />
+        </conditional>
+    </xml>
+
+    <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:
+                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
+                #end if
+            #end if
+        #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 argument="--minMappingQuality" type="integer" optional="true" value="" 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."/>
+    </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="xMax">
+        <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
+            label="Max value for the x-axis in counts per bin" />
+    </xml>
+
+    <xml name="filterThreshold">
+        <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
+            label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
+
+        <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
+            label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
+    </xml>
+
+    <xml name="pseudocount">
+        <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+    </xml>
+    <xml name='matrix_h5_cooler_macro'>
+        <param name='matrix_h5_cooler' type="data" format="h5,cool"
+            label="Matrix to compute on"/>
+    </xml>
+    <xml name='matrix_h5_cooler_multiple_macro'>
+        <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
+            label="Matricies to compute on" multiple="true"/>
+    </xml>
+    <token name="@REFERENCES@">
+
+.. class:: infomark
+
+For more information on the tools, please visit our `help site`_.
+
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+
+This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+
+.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
+.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
+.. _help site: https://hicexplorer.readthedocs.org
+
+    </token>
+
+
+    <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>
+    </xml>
+
+    <xml name="multiple_input_bigwigs">
+        <repeat name="input_files" title="BigWig files" min="2">
+            <param name="bigwigfile" type="data" format="bigwig"
+                label="Bigwig file"
+                help="The Bigwig 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>
+    </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())
+        #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)
+
+            ##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
+        #end for
+    </token>
+
+    <token name="@multiple_input_bigwigs@">
+        #import tempfile
+        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+        #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 $temp_input_handle.close()
+            #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
+            #silent $files.append('%s.bw' % $temp_input_path)
+
+            ##set $files += [str($i.bigwigfile)]
+            #if str($i.label.value) != "":
+                #set $labels += ["\"%s\"" % ($i.label.value)]
+            #else
+                #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
+            #end if
+        #end for
+    </token>
+
+    <xml name="reference_genome_source">
+        <conditional name="source">
+            <param name="ref_source" type="select" label="Reference genome">
+                <option value="cached">locally cached</option>
+                <option value="history">in your history</option>
+            </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">
+                        <filter type="sort_by" column="1" />
+                        <validator type="no_options" message="No indexes are available." />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@reference_genome_source@">
+    #if $source.ref_source=="history":
+        --genome $source.input1
+    #else:
+        --genome "${source.input1_2bit.fields.path}"
+    #end if
+    </token>
+
+    <xml name="effectiveGenomeSize">
+        <conditional name="effectiveGenomeSize">
+            <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.">
+                <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="specific">user specified</option>
+            </param>
+            <when value="specific">
+                <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
+            </when>
+            <when value="2150570000" />
+            <when value="2451960000" />
+            <when value="121400000" />
+            <when value="93260000" />
+        </conditional>
+    </xml>
+
+    <xml name="image_file_format">
+        <param name="outFileFormat" type="select" label="Image file format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="eps">eps</option>
+            <option value="emf">emf</option>
+        </param>
+    </xml>
+
+    <xml name="missingDataAsZero">
+                <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 treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+    </xml>
+
+    <xml name="input_save_matrix_values">
+        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+    </xml>
+
+    <xml name="input_graphic_output_settings">
+        <conditional name="output" >
+            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <yield />
+                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
+                <param name="saveSortedRegions" type="boolean" 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."/>
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="input_image_file_format">
+        <param name="outFileFormat" type="select" label="Image file format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="eps">eps</option>
+            <option value="emf">emf</option>
+        </param>
+    </xml>
+
+    <xml name="output_image_file_format">
+        <data format="png" name="outFileName" label="${tool.name} image">
+            <change_format>
+                <when input="output.outFileFormat" value="pdf" format="pdf" />
+                <when input="output.outFileFormat" value="svg" format="svg" />
+                <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="emf" format="emf" />
+            </change_format>
+        </data>
+    </xml>
+
+    <xml name="output_save_matrix_values">
+        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveMatrix'] is True
+            ))
+            </filter>
+        </data>
+    </xml>
+
+    <xml name="output_graphic_outputs">
+        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveData'] is True
+            ))
+            </filter>
+        </data>
+        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveSortedRegions'] is True
+            ))
+            </filter>
+        </data>
+    </xml>
+
+    <xml name="track_input_h5_macro">
+        <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
+    </xml>
+    <xml name="track_input_bed_macro">
+        <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
+    </xml>
+    <xml name="track_input_bedgraph_macro">
+        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
+    </xml>
+    <xml name="track_input_bigwig_macro">
+        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
+    </xml>
+    <xml name="track_input_bedgraph_matrix_macro">
+        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
+    </xml>
+    <xml name="track_input_tabular_macro">
+        <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
+    </xml>
+    <xml name="plot_title">
+        <param name="title" type="text" optional="true" label="Plot title"/>
+    </xml>
+
+    <xml name="spacer_macro">
+        <param name="spacer_width" type="float" value="" optional="True"
+              label="Include spacer at the end of the track." help="Width of the spacer." />
+    </xml>
+    <xml name="fontsize_macro">
+        <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+    </xml>
+</macros>
Binary file test-data/Li_chrX30-35_cool.png has changed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiFDR_boundaries.bed	Wed Mar 07 03:39:03 2018 -0500
@@ -0,0 +1,2 @@
+chr2L	22922500	22927500	B04585	-0.068256362891	.
+chrX	87500	92500	B19358	-0.072020401017	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiFDR_boundaries.gff	Wed Mar 07 03:39:03 2018 -0500
@@ -0,0 +1,2 @@
+chr2L	HiCExplorer	boundary	22922500	22927500	-0.068256362891	.	.	ID=B04585;delta=0.021954846720;pvalue=0.000033964776;tad_sep=-0.068256362891
+chrX	HiCExplorer	boundary	87500	92500	-0.072020401017	.	.	ID=B19358;delta=0.019799980104;pvalue=0.000055223433;tad_sep=-0.072020401017
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiFDR_score.bedgraph	Wed Mar 07 03:39:03 2018 -0500
@@ -0,0 +1,23814 @@
+chr2L	2500	7500	-0.164488846397
+chr2L	7500	12500	0.004155516280
+chr2L	12500	17500	0.260509497302
+chr2L	17500	22500	0.126728724578
+chr2L	22500	27500	0.107536542495
+chr2L	27500	32500	0.067996441287
+chr2L	32500	37500	0.180067325085
+chr2L	37500	42500	0.188704045555
+chr2L	42500	47500	0.123071283383
+chr2L	47500	52500	0.090946822420
+chr2L	52500	57500	0.050290136708
+chr2L	57500	62500	0.043738171585
+chr2L	62500	67500	0.036458137676
+chr2L	67500	72500	-0.008311665224
+chr2L	72500	77500	-0.025506335364
+chr2L	77500	82500	-0.028782499450
+chr2L	82500	87500	-0.008859983289
+chr2L	87500	92500	0.012581289189
+chr2L	92500	97500	-0.026656341295
+chr2L	97500	102500	-0.064470557052
+chr2L	102500	107500	-0.022699733707
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+chr2L	117500	122500	-0.006876513913
+chr2L	122500	127500	0.016147318959
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+chr2L	167500	172500	0.029002777185
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+chr2L	187500	192500	0.010495785312
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+chr2L	197500	202500	-0.039867994837
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+chr2L	217500	222500	-0.036501614110
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+chr2L	227500	232500	-0.023335648652
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+chr2L	272500	277500	-0.059012201761
+chr2L	277500	282500	-0.086006441495
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+chr2L	287500	292500	-0.053031533287
+chr2L	292500	297500	-0.083051915395
+chr2L	297500	302500	-0.083051915395
+chr2L	302500	307500	-0.051758175573
+chr2L	307500	312500	-0.044639541179
+chr2L	312500	317500	-0.043712800180
+chr2L	317500	322500	-0.019156222003
+chr2L	322500	327500	-0.017442079268
+chr2L	327500	332500	0.041070352715
+chr2L	332500	337500	0.049256940562
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+chr2L	342500	347500	0.053147123147
+chr2L	347500	352500	0.078905602777
+chr2L	352500	357500	0.093459536727
+chr2L	357500	362500	0.079684892703
+chr2L	362500	367500	0.063143859889
+chr2L	367500	372500	0.092016050812
+chr2L	372500	377500	0.061075544744
+chr2L	377500	382500	0.013498603323
+chr2L	382500	387500	0.029781933737
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+chr2L	427500	432500	-0.021015012893
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+chr2L	442500	447500	-0.064964420946
+chr2L	447500	452500	-0.051664858126
+chr2L	452500	457500	-0.071914886809
+chr2L	457500	462500	-0.069724393991
+chr2L	462500	467500	-0.069724393991
+chr2L	467500	472500	-0.059605045512
+chr2L	472500	477500	-0.051309772332
+chr2L	477500	482500	-0.048373705573
+chr2L	482500	487500	-0.048373705573
+chr2L	487500	492500	-0.014227247533
+chr2L	492500	497500	-0.064541001831
+chr2L	497500	502500	-0.064541001831
+chr2L	502500	507500	-0.056245728652
+chr2L	507500	512500	-0.064541001831
+chr2L	512500	517500	-0.071946857401
+chr2L	517500	522500	-0.071946857401
+chr2L	522500	527500	-0.071946857401
+chr2L	527500	532500	-0.076979302876
+chr2L	532500	537500	-0.076979302876
+chr2L	537500	542500	-0.076979302876
+chr2L	542500	547500	-0.120135452320
+chr2L	547500	552500	-0.107649833515
+chr2L	552500	557500	-0.087399804832
+chr2L	557500	562500	-0.099885423637
+chr2L	562500	567500	-0.099885423637
+chr2L	567500	572500	-0.099885423637
+chr2L	572500	577500	-0.099885423637
+chr2L	577500	582500	-0.099885423637
+chr2L	582500	587500	-0.084057834311
+chr2L	587500	592500	-0.084057834311
+chr2L	592500	597500	-0.065926294209
+chr2L	597500	602500	-0.076626770847
+chr2L	602500	607500	-0.063204938090
+chr2L	607500	612500	-0.066951827756
+chr2L	612500	617500	-0.066951827756
+chr2L	617500	622500	-0.095049772135
+chr2L	622500	627500	-0.086559234121
+chr2L	627500	632500	-0.104690774223
+chr2L	632500	637500	-0.104690774223
+chr2L	637500	642500	-0.104690774223
+chr2L	642500	647500	-0.104690774223
+chr2L	647500	652500	-0.053713171413
+chr2L	652500	657500	-0.032383933202
+chr2L	657500	662500	-0.013390883314
+chr2L	662500	667500	-0.023624746219
+chr2L	667500	672500	-0.015426022630
+chr2L	672500	677500	-0.013822637003
+chr2L	677500	682500	-0.013822637003
+chr2L	682500	687500	-0.028847855386
+chr2L	687500	692500	0.017132537265
+chr2L	692500	697500	0.017132537265
+chr2L	697500	702500	0.045710448555
+chr2L	702500	707500	0.027583820124
+chr2L	707500	712500	-0.028547755658
+chr2L	712500	717500	-0.000317643464
+chr2L	717500	722500	-0.014643992043
+chr2L	722500	727500	-0.014643992043
+chr2L	727500	732500	-0.017732383711
+chr2L	732500	737500	0.001546317552
+chr2L	737500	742500	-0.014947679217
+chr2L	742500	747500	-0.007136697412
+chr2L	747500	752500	-0.023340488177
+chr2L	752500	757500	-0.003090459494
+chr2L	757500	762500	-0.002431239390
+chr2L	762500	767500	0.019169021058
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+chr2L	19177500	19182500	-0.084855325928
+chr2L	19182500	19187500	-0.078728520897
+chr2L	19187500	19192500	-0.063993214854
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+chr2L	19197500	19202500	-0.050236119093
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+chr2R	19057500	19062500	0.127572041263
+chr2R	19062500	19067500	0.121148966597
+chr2R	19067500	19072500	0.069402888538
+chr2R	19072500	19077500	0.073690573941
+chr2R	19077500	19082500	0.037636363882
+chr2R	19082500	19087500	0.002894545093
+chr2R	19087500	19092500	0.022426070152
+chr2R	19092500	19097500	0.027119059451
+chr2R	19097500	19102500	0.001000405123
+chr2R	19102500	19107500	-0.004672787976
+chr2R	19107500	19112500	-0.017977429641
+chr2R	19112500	19117500	-0.013163919868
+chr2R	19117500	19122500	-0.021164091170
+chr2R	19122500	19127500	-0.018353838671
+chr2R	19127500	19132500	-0.015793433325
+chr2R	19132500	19137500	-0.022227769426
+chr2R	19137500	19142500	-0.004650133002
+chr2R	19142500	19147500	-0.023374666792
+chr2R	19147500	19152500	-0.029518040834
+chr2R	19152500	19157500	-0.019063645029
+chr2R	19157500	19162500	-0.010757950980
+chr2R	19162500	19167500	-0.005917184622
+chr2R	19167500	19172500	-0.016371580427
+chr2R	19172500	19177500	-0.016371580427
+chr2R	19177500	19182500	-0.009613437497
+chr2R	19182500	19187500	0.020143880570
+chr2R	19187500	19192500	0.033376592197
+chr2R	19192500	19197500	0.056692174141
+chr2R	19197500	19202500	0.067436846066
+chr2R	19202500	19207500	0.102399394347
+chr2R	19207500	19212500	0.064217331869
+chr2R	19212500	19217500	0.060610640326
+chr2R	19217500	19222500	0.053474512062
+chr2R	19222500	19227500	0.064542456493
+chr2R	19227500	19232500	0.042696923957
+chr2R	19232500	19237500	-0.012364576790
+chr2R	19237500	19242500	0.000177508995
+chr2R	19242500	19247500	-0.016015053254
+chr2R	19247500	19252500	-0.028374338168
+chr2R	19252500	19257500	-0.012710252670
+chr2R	19257500	19262500	-0.019762948505
+chr2R	19262500	19267500	0.011061364103
+chr2R	19267500	19272500	0.004872058285
+chr2R	19272500	19277500	-0.046988690713
+chr2R	19277500	19282500	-0.014753718149
+chr2R	19282500	19287500	-0.028488851252
+chr2R	19287500	19292500	-0.028488851252
+chr2R	19292500	19297500	-0.032465588340
+chr2R	19297500	19302500	-0.011593502404
+chr2R	19302500	19307500	-0.017723056506
+chr2R	19307500	19312500	-0.021841550151
+chr2R	19312500	19317500	-0.026012398220
+chr2R	19317500	19322500	-0.031615577000
+chr2R	19322500	19327500	0.050816486921
+chr2R	19327500	19332500	0.095123256371
+chr2R	19332500	19337500	0.103885686852
+chr2R	19337500	19342500	0.079754746086
+chr2R	19342500	19347500	0.101247200063
+chr2R	19347500	19352500	0.101247200063
+chr2R	19352500	19357500	0.108677343353
+chr2R	19357500	19362500	0.090791580918
+chr2R	19362500	19367500	0.090791580918
+chr2R	19367500	19372500	0.066057726620
+chr2R	19372500	19377500	0.050761079679
+chr2R	19377500	19382500	0.040700338310
+chr2R	19382500	19387500	0.003943591613
+chr2R	19387500	19392500	0.004258812576
+chr2R	19392500	19397500	0.004366213171
+chr2R	19397500	19402500	-0.030073303622
+chr2R	19402500	19407500	-0.048609026362
+chr2R	19407500	19412500	-0.062644612193
+chr2R	19412500	19417500	-0.056870943299
+chr2R	19417500	19422500	-0.051369318577
+chr2R	19422500	19427500	-0.051369318577
+chr2R	19427500	19432500	-0.086294576933
+chr2R	19432500	19437500	-0.090140586176
+chr2R	19437500	19442500	-0.055412301188
+chr2R	19442500	19447500	-0.052987249396
+chr2R	19447500	19452500	-0.068806933855
+chr2R	19452500	19457500	-0.063551236363
+chr2R	19457500	19462500	-0.063551236363
+chr2R	19462500	19467500	-0.048905631449
+chr2R	19467500	19472500	-0.048905631449
+chr2R	19472500	19477500	-0.065098193698
+chr2R	19477500	19482500	-0.038079123718
+chr2R	19482500	19487500	0.008542091498
+chr2R	19487500	19492500	0.021845181835
+chr2R	19492500	19497500	0.026772451401
+chr2R	19497500	19502500	0.050577558655
+chr2R	19502500	19507500	0.052282111965
+chr2R	19507500	19512500	0.055469305460
+chr2R	19512500	19517500	0.014274387232
+chr2R	19517500	19522500	0.004213645862
+chr2R	19522500	19527500	-0.006102297112
+chr2R	19527500	19532500	-0.006102297112
+chr2R	19532500	19537500	-0.006102297112
+chr2R	19537500	19542500	-0.034702034389
+chr2R	19542500	19547500	-0.032355014498
+chr2R	19547500	19552500	-0.015289775426
+chr2R	19552500	19557500	-0.015289775426
+chr2R	19557500	19562500	-0.046695918309
+chr2R	19562500	19567500	-0.051280781853
+chr2R	19567500	19572500	-0.051280781853
+chr2R	19572500	19577500	-0.079165251308
+chr2R	19577500	19582500	-0.107133618290
+chr2R	19582500	19587500	-0.106876317050
+chr2R	19587500	19592500	-0.106876317050
+chr2R	19592500	19597500	-0.106876317050
+chr2R	19597500	19602500	-0.084229341555
+chr2R	19602500	19607500	-0.073161239422
+chr2R	19607500	19612500	-0.068089915720
+chr2R	19612500	19617500	-0.049820688858
+chr2R	19617500	19622500	-0.063856274689
+chr2R	19622500	19627500	-0.063856274689
+chr2R	19627500	19632500	-0.063856274689
+chr2R	19632500	19637500	-0.049090596379
+chr2R	19637500	19642500	-0.049090596379
+chr2R	19642500	19647500	-0.049090596379
+chr2R	19647500	19652500	-0.022016032552
+chr2R	19652500	19657500	-0.022016032552
+chr2R	19657500	19662500	-0.007805432819
+chr2R	19662500	19667500	-0.014494364563
+chr2R	19667500	19672500	-0.038769839724
+chr2R	19672500	19677500	-0.011431163556
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+chr2R	19682500	19687500	0.070217291869
+chr2R	19687500	19692500	0.067986015596
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+chr2R	19707500	19712500	0.095479004470
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+chr2R	19717500	19722500	0.007279712727
+chr2R	19722500	19727500	-0.019994322492
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+chr2R	19732500	19737500	-0.024505684009
+chr2R	19737500	19742500	-0.067228489882
+chr2R	19742500	19747500	-0.068724806402
+chr2R	19747500	19752500	-0.050570990775
+chr2R	19752500	19757500	-0.041959601112
+chr2R	19757500	19762500	-0.036382038010
+chr2R	19762500	19767500	-0.036382038010
+chr2R	19767500	19772500	-0.066544505349
+chr2R	19772500	19777500	-0.066544505349
+chr2R	19777500	19782500	-0.066544505349
+chr2R	19782500	19787500	-0.104579209824
+chr2R	19787500	19792500	-0.099872063799
+chr2R	19792500	19797500	-0.099872063799
+chr2R	19797500	19802500	-0.070115978844
+chr2R	19802500	19807500	-0.070115978844
+chr2R	19807500	19812500	-0.070115978844
+chr2R	19812500	19817500	-0.063864751398
+chr2R	19817500	19822500	-0.063864751398
+chr2R	19822500	19827500	-0.063864751398
+chr2R	19827500	19832500	-0.046053920265
+chr2R	19832500	19837500	-0.018758054528
+chr2R	19837500	19842500	-0.018758054528
+chr2R	19842500	19847500	-0.034622699208
+chr2R	19847500	19852500	-0.019734409612
+chr2R	19852500	19857500	-0.006429767946
+chr2R	19857500	19862500	-0.006429767946
+chr2R	19862500	19867500	0.020175130698
+chr2R	19867500	19872500	0.028772626339
+chr2R	19872500	19877500	0.012418063725
+chr2R	19877500	19882500	-0.012532252201
+chr2R	19882500	19887500	-0.012532252201
+chr2R	19887500	19892500	-0.012532252201
+chr2R	19892500	19897500	-0.009804854900
+chr2R	19897500	19902500	0.022204980035
+chr2R	19902500	19907500	0.027629176203
+chr2R	19907500	19912500	-0.017814868309
+chr2R	19912500	19917500	-0.030384181122
+chr2R	19917500	19922500	-0.048622007206
+chr2R	19922500	19927500	-0.061926648871
+chr2R	19927500	19932500	-0.060460375854
+chr2R	19932500	19937500	-0.041898380396
+chr2R	19937500	19942500	-0.045075649758
+chr2R	19942500	19947500	-0.049050494220
+chr2R	19947500	19952500	-0.027178824652
+chr2R	19952500	19957500	-0.018567434989
+chr2R	19957500	19962500	-0.027178824652
+chr2R	19962500	19967500	0.018215509973
+chr2R	19967500	19972500	0.018215509973
+chr2R	19972500	19977500	0.018215509973
+chr2R	19977500	19982500	-0.010526684645
+chr2R	19982500	19987500	-0.010526684645
+chr2R	19987500	19992500	0.007407179015
+chr2R	19992500	19997500	0.027033763935
+chr2R	19997500	20002500	-0.028218123743
+chr2R	20002500	20007500	-0.018400965913
+chr2R	20007500	20012500	-0.037847583689
+chr2R	20012500	20017500	-0.065753335100
+chr2R	20017500	20022500	-0.065753335100
+chr2R	20022500	20027500	-0.048777408286
+chr2R	20027500	20032500	-0.052803934405
+chr2R	20032500	20037500	-0.052803934405
+chr2R	20037500	20042500	-0.052803934405
+chr2R	20042500	20047500	-0.062621092236
+chr2R	20047500	20052500	-0.044737652997
+chr2R	20052500	20057500	-0.044737652997
+chr2R	20057500	20062500	-0.059614144996
+chr2R	20062500	20067500	-0.080503817521
+chr2R	20067500	20072500	-0.061087047683
+chr2R	20072500	20077500	-0.057668548230
+chr2R	20077500	20082500	-0.057668548230
+chr2R	20082500	20087500	-0.051770215026
+chr2R	20087500	20092500	0.005316704202
+chr2R	20092500	20097500	0.005316704202
+chr2R	20097500	20102500	-0.000693883164
+chr2R	20102500	20107500	-0.000693883164
+chr2R	20107500	20112500	0.021161573552
+chr2R	20112500	20117500	0.053750468713
+chr2R	20117500	20122500	0.062773974586
+chr2R	20122500	20127500	0.036244184257
+chr2R	20127500	20132500	0.038222579347
+chr2R	20132500	20137500	0.038222579347
+chr2R	20137500	20142500	0.038222579347
+chr2R	20142500	20147500	0.040300779491
+chr2R	20147500	20152500	-0.015103882672
+chr2R	20152500	20157500	-0.031780920637
+chr2R	20157500	20162500	-0.040115953783
+chr2R	20162500	20167500	-0.040115953783
+chr2R	20167500	20172500	-0.027548106559
+chr2R	20172500	20177500	-0.025220429491
+chr2R	20177500	20182500	-0.015221642143
+chr2R	20182500	20187500	-0.015221642143
+chr2R	20187500	20192500	-0.006610252480
+chr2R	20192500	20197500	-0.004329917839
+chr2R	20197500	20202500	-0.015221642143
+chr2R	20202500	20207500	-0.015221642143
+chr2R	20207500	20212500	-0.003417332585
+chr2R	20212500	20217500	-0.024307005110