# HG changeset patch
# User bgruening
# Date 1470911333 14400
# Node ID 96057da0d8d8147d1d2dc7a5c214bfdedaf287bc
# Parent  eab93a5553ec4e8e49dc7509943d802ef8ad69bf
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296

diff -r eab93a5553ec -r 96057da0d8d8 bamCoverage.xml
--- a/bamCoverage.xml	Fri May 13 17:13:52 2016 -0400
+++ b/bamCoverage.xml	Thu Aug 11 06:28:53 2016 -0400
@@ -50,6 +50,12 @@
                 #if str($advancedOpt.filterRNAstrand) != 'no':
                     --filterRNAstrand '$advancedOpt.filterRNAstrand'
                 #end if
+
+                #if $advancedOpt.Offset:
+                    --Offset '$advancedOpt.Offset'
+                #end if
+
+                @blacklist@
             #end if
 ]]>
     </command>
@@ -107,7 +113,19 @@
 
                 <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." />
+                    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. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options." />
+
+                <param argument="--Offset" type="integer"  value="" optional="True"
+                    label="Offset inside each alignment to use for the signal location."
+                    help="Uses this offset inside of each read as the signal. This is useful in
+                        cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
+                        should be used to denote where the signal is (rather than the span of the
+                        whole alignment). This can be paired with the --filterRNAstrand option. Note
+                        that negative values indicate offsets from the end of each read. A value of
+                        1 indicates the first base of the alignment (taking alignment orientation
+                        into account). Likewise, a value of -1 is the last base of the alignment. An
+                        offset of 0 is not permitted. By default, the entire alignment is used to
+                        denote where the signal is located." />
 
                 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
                     help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
@@ -116,6 +134,7 @@
                     <option value="forward">forward</option>
                     <option value="reverse">reverse</option>
                 </param>
+                <expand macro="blacklist" />
 
             </when>
         </conditional>
diff -r eab93a5553ec -r 96057da0d8d8 deepTools_macros.xml
--- a/deepTools_macros.xml	Fri May 13 17:13:52 2016 -0400
+++ b/deepTools_macros.xml	Thu Aug 11 06:28:53 2016 -0400
@@ -30,6 +30,25 @@
         #if $advancedOpt.samFlagExclude:
             --samFlagExclude $advancedOpt.samFlagExclude
         #end if
+        #if $advancedOpt.minFragmentLength:
+            --minFragmentLength $advancedOpt.minFragmentLength
+        #end if
+        #if $advancedOpt.maxFragmentLength:
+            --maxFragmentLength $advancedOpt.maxFragmentLength
+        #end if
+    </token>
+
+    <token name="@ADVANCED_OPTS_GTF@">
+        $advancedOpt.metagene
+        #if $advancedOpt.transcriptID:
+            --transcriptID $advancedOpt.transcriptID
+        #end if
+        #if $advancedOpt.exonID:
+            --exonID $advancedOpt.exonID
+        #end if
+        #if $advancedOpt.transcript_id_designator:
+            --transcript_id_designator $advancedOpt.transcript_id_designator
+        #end if
     </token>
 
     <xml name="heatmap_options">
@@ -59,9 +78,9 @@
     </xml>
 
     <xml name="zMin_zMax">
-        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
+        <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
             help="If not specified the value is set automatically."/>
-        <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
+        <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
             help="If not specified the value is set automatically."/>
     </xml>
 
@@ -159,14 +178,43 @@
             help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
     </xml>
 
+    <xml name="fragLength">
+        <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
+            label="Minimum fragment length for inclusion."
+            help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
+        <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
+            label="Maximum fragment length for inclusion."
+            help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
+    </xml>
+
     <xml name="read_processing_options">
         <expand macro="extendReads" />
         <expand macro="ignoreDuplicates" />
         <expand macro="centerReads" />
         <expand macro="minMappingQuality" />
         <expand macro="samFlags" />
+        <expand macro="fragLength" />
     </xml>
 
+    <xml name="gtf_options">
+        <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
+            label="Use a metagene model"
+            help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
+        <param argument="--transcriptID" optional="True" value="transcript" type="text"
+            label="trascript designator"
+            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
+        <param argument="--exonID" optional="True" value="exon" type="text"
+            label="exon designator"
+            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
+        <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
+            label="transcriptID key designator"
+            help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
+                  or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
+                  as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
+                  convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
+    </xml>
+
+
     <xml name="plotNumbers">
         <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
             label="Plot the correlation value"
@@ -247,7 +295,7 @@
     </xml>
 
     <xml name="minMappingQuality">
-        <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
+        <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."/>
     </xml>
@@ -363,6 +411,47 @@
 ]]>
     </token>
 
+    <xml name="blacklist">
+        <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
+            label="Blacklisted regions in BED/GTF format"
+            help="One or more files containing regions to exclude from the analysis" />
+    </xml>
+
+    <token name="@blacklist@">
+<![CDATA[
+        #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
+            #set blfiles=[]
+            #for $f in $advancedOpt.blackListFileName:
+                #silent $blfiles.append("'%s'" % $f)
+            #end for
+            #if $blfiles != ["'None'"]:
+                --blackListFileName #echo ' '.join($blfiles)#
+            #end if
+        #end if
+]]> 
+    </token>
+
+    <xml name="multiple_bed">
+        <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
+            label="Regions in BED/GTF format"
+            help="One or more files containing regions to include in the analysis" />
+    </xml>
+
+    <token name="@multiple_bed@">
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+        #for $f in $BED:
+            #silent $files.append("'%s'" % $f)
+            #silent $labels.append("'%s'" % $f.display_name)
+        #end for
+        #if len($files) > 0:
+            --BED #echo ' '.join($files)#
+            --regionLabels #echo ' '.join($labels)#
+        #end if
+]]> 
+    </token>
+
     <xml name="reference_genome_source">
         <conditional name="source">
             <param name="ref_source" type="select" label="Reference genome">
@@ -404,7 +493,8 @@
                 <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"/>
+                <param argument="--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" />
@@ -439,7 +529,10 @@
             <when value="no" />
             <when value="yes">
                 <yield />
-                <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."/>
+                <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>
@@ -454,6 +547,11 @@
         </param>
     </xml>
 
+    <xml name="output_dpi">
+        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
+            label="Image dpi" help=""/>
+    </xml>
+
     <xml name="output_image_file_format">
         <data format="png" name="outFileName" label="${tool.name} image">
             <change_format>
@@ -497,7 +595,9 @@
     </xml>
 
     <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">
+        <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">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>
             <option value="Spectral">Spectral</option>
diff -r eab93a5553ec -r 96057da0d8d8 static/images/plotEnrichment_output.png
Binary file static/images/plotEnrichment_output.png has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCompare_result1.bg
--- a/test-data/bamCompare_result1.bg	Fri May 13 17:13:52 2016 -0400
+++ b/test-data/bamCompare_result1.bg	Thu Aug 11 06:28:53 2016 -0400
@@ -1,1 +1,1 @@
-chrM	0	16569	1.0
+chrM	0	16569	1.00
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Fri May 13 17:13:52 2016 -0400
+++ b/test-data/bamCoverage_result3.bg	Thu Aug 11 06:28:53 2016 -0400
@@ -1,8 +1,7 @@
-chrM	0	10	18498299.57
-chrM	10	200	9768764.94
-chrM	200	210	10184457.07
-chrM	210	220	9976611.00
+chrM	0	210	9768764.94
+chrM	210	220	9560918.88
 chrM	220	230	7690304.31
-chrM	230	240	6027535.81
+chrM	230	240	5196151.56
 chrM	240	250	3325537.00
 chrM	250	260	623538.19
+chrM	260	16569	0.00
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg	Fri May 13 17:13:52 2016 -0400
+++ b/test-data/bamCoverage_result4.bg	Thu Aug 11 06:28:53 2016 -0400
@@ -1,472 +1,472 @@
-phiX174	0	10	16038.46
-phiX174	10	20	48115.38
-phiX174	20	70	144346.15
-phiX174	70	80	192461.54
-phiX174	80	90	176423.08
-phiX174	90	100	160384.62
-phiX174	100	120	112269.23
-phiX174	120	140	144346.15
-phiX174	140	150	160384.62
-phiX174	150	160	128307.69
-phiX174	160	170	160384.62
-phiX174	170	180	176423.08
-phiX174	180	200	208500.00
-phiX174	200	210	192461.54
-phiX174	210	220	240576.92
-phiX174	220	230	272653.85
-phiX174	230	240	336807.69
-phiX174	240	250	320769.23
-phiX174	250	260	288692.31
-phiX174	260	270	336807.69
-phiX174	270	280	400961.54
-phiX174	280	300	417000.00
-phiX174	300	310	352846.15
-phiX174	310	320	320769.23
-phiX174	320	330	368884.62
-phiX174	330	340	352846.15
-phiX174	340	350	288692.31
-phiX174	350	360	256615.38
-phiX174	360	370	224538.46
-phiX174	370	380	240576.92
-phiX174	380	390	304730.77
-phiX174	390	400	256615.38
-phiX174	400	410	240576.92
-phiX174	410	420	224538.46
-phiX174	420	450	288692.31
-phiX174	450	460	304730.77
-phiX174	460	470	336807.69
-phiX174	470	490	417000.00
-phiX174	490	510	497192.31
-phiX174	510	520	465115.38
-phiX174	520	530	561346.15
-phiX174	530	540	497192.31
-phiX174	540	550	529269.23
-phiX174	550	560	545307.69
-phiX174	560	570	641538.46
-phiX174	570	580	625500.00
-phiX174	580	590	561346.15
-phiX174	590	600	609461.54
-phiX174	600	610	545307.69
-phiX174	610	630	625500.00
-phiX174	630	640	577384.62
-phiX174	640	650	513230.77
-phiX174	650	660	545307.69
-phiX174	660	670	561346.15
-phiX174	670	680	593423.08
-phiX174	680	690	657576.92
-phiX174	690	700	641538.46
-phiX174	700	710	561346.15
-phiX174	710	730	593423.08
-phiX174	730	740	513230.77
-phiX174	740	760	593423.08
-phiX174	760	770	497192.31
-phiX174	770	780	513230.77
-phiX174	780	790	529269.23
-phiX174	790	800	545307.69
-phiX174	800	810	449076.92
-phiX174	810	820	433038.46
-phiX174	820	830	368884.62
-phiX174	830	840	320769.23
-phiX174	840	850	352846.15
-phiX174	850	860	304730.77
-phiX174	860	870	336807.69
-phiX174	870	880	256615.38
-phiX174	880	890	352846.15
-phiX174	890	900	384923.08
-phiX174	900	910	465115.38
-phiX174	910	920	545307.69
-phiX174	920	930	561346.15
-phiX174	930	940	545307.69
-phiX174	940	950	577384.62
-phiX174	950	960	593423.08
-phiX174	960	970	513230.77
-phiX174	970	980	481153.85
-phiX174	980	990	433038.46
-phiX174	990	1000	417000.00
-phiX174	1000	1010	449076.92
-phiX174	1010	1030	577384.62
-phiX174	1030	1040	753807.69
-phiX174	1040	1050	785884.62
-phiX174	1050	1060	817961.54
-phiX174	1060	1070	866076.92
-phiX174	1070	1080	834000.00
-phiX174	1080	1090	866076.92
-phiX174	1090	1100	769846.15
-phiX174	1100	1110	737769.23
-phiX174	1110	1120	657576.92
-phiX174	1120	1130	641538.46
-phiX174	1130	1140	625500.00
-phiX174	1140	1150	673615.38
-phiX174	1150	1160	625500.00
-phiX174	1160	1170	593423.08
-phiX174	1170	1180	609461.54
-phiX174	1180	1190	577384.62
-phiX174	1190	1200	513230.77
-phiX174	1200	1210	481153.85
-phiX174	1210	1220	561346.15
-phiX174	1220	1230	481153.85
-phiX174	1230	1240	449076.92
-phiX174	1240	1250	352846.15
-phiX174	1250	1260	336807.69
-phiX174	1260	1270	400961.54
-phiX174	1270	1280	352846.15
-phiX174	1280	1290	368884.62
-phiX174	1290	1300	320769.23
-phiX174	1300	1310	384923.08
-phiX174	1310	1320	513230.77
-phiX174	1320	1330	497192.31
-phiX174	1330	1340	513230.77
-phiX174	1340	1350	481153.85
-phiX174	1350	1370	497192.31
-phiX174	1370	1390	465115.38
-phiX174	1390	1400	352846.15
-phiX174	1400	1410	449076.92
-phiX174	1410	1430	481153.85
-phiX174	1430	1450	545307.69
-phiX174	1450	1460	561346.15
-phiX174	1460	1470	577384.62
-phiX174	1470	1480	609461.54
-phiX174	1480	1490	593423.08
-phiX174	1490	1500	545307.69
-phiX174	1500	1510	657576.92
-phiX174	1510	1520	625500.00
-phiX174	1520	1540	785884.62
-phiX174	1540	1550	721730.77
-phiX174	1550	1570	753807.69
-phiX174	1570	1580	769846.15
-phiX174	1580	1590	673615.38
-phiX174	1590	1600	625500.00
-phiX174	1600	1610	561346.15
-phiX174	1610	1620	529269.23
-phiX174	1620	1630	497192.31
-phiX174	1630	1640	465115.38
-phiX174	1640	1650	481153.85
-phiX174	1650	1660	497192.31
-phiX174	1660	1670	529269.23
-phiX174	1670	1680	593423.08
-phiX174	1680	1690	513230.77
-phiX174	1690	1700	529269.23
-phiX174	1700	1710	593423.08
-phiX174	1710	1720	545307.69
-phiX174	1720	1730	529269.23
-phiX174	1730	1740	577384.62
-phiX174	1740	1750	529269.23
-phiX174	1750	1760	433038.46
-phiX174	1760	1770	417000.00
-phiX174	1770	1780	368884.62
-phiX174	1780	1790	352846.15
-phiX174	1790	1810	336807.69
-phiX174	1810	1820	320769.23
-phiX174	1820	1830	465115.38
-phiX174	1830	1860	705692.31
-phiX174	1860	1870	801923.08
-phiX174	1870	1880	737769.23
-phiX174	1880	1890	673615.38
-phiX174	1890	1900	705692.31
-phiX174	1900	1910	609461.54
-phiX174	1910	1920	400961.54
-phiX174	1920	1930	465115.38
-phiX174	1930	1940	545307.69
-phiX174	1940	1950	449076.92
-phiX174	1950	1960	481153.85
-phiX174	1960	1970	529269.23
-phiX174	1970	1980	673615.38
-phiX174	1980	1990	641538.46
-phiX174	1990	2000	657576.92
-phiX174	2000	2010	673615.38
-phiX174	2010	2020	641538.46
-phiX174	2020	2030	657576.92
-phiX174	2030	2050	673615.38
-phiX174	2050	2060	481153.85
-phiX174	2060	2070	513230.77
-phiX174	2070	2080	481153.85
-phiX174	2080	2100	513230.77
-phiX174	2100	2110	529269.23
-phiX174	2110	2120	513230.77
-phiX174	2120	2130	529269.23
-phiX174	2130	2140	545307.69
-phiX174	2140	2150	513230.77
-phiX174	2150	2160	545307.69
-phiX174	2160	2170	417000.00
-phiX174	2170	2180	352846.15
-phiX174	2180	2190	433038.46
-phiX174	2190	2200	449076.92
-phiX174	2200	2210	433038.46
-phiX174	2210	2220	481153.85
-phiX174	2220	2230	545307.69
-phiX174	2230	2240	593423.08
-phiX174	2240	2250	625500.00
-phiX174	2250	2260	721730.77
-phiX174	2260	2270	625500.00
-phiX174	2270	2290	593423.08
-phiX174	2290	2300	609461.54
-phiX174	2300	2310	737769.23
-phiX174	2310	2320	769846.15
-phiX174	2320	2330	866076.92
-phiX174	2330	2340	850038.46
-phiX174	2340	2350	898153.85
-phiX174	2350	2360	801923.08
-phiX174	2360	2370	914192.31
-phiX174	2370	2380	801923.08
-phiX174	2380	2390	641538.46
-phiX174	2390	2400	593423.08
-phiX174	2400	2410	417000.00
-phiX174	2410	2420	400961.54
-phiX174	2420	2430	352846.15
-phiX174	2430	2440	481153.85
-phiX174	2440	2450	449076.92
-phiX174	2450	2460	609461.54
-phiX174	2460	2470	673615.38
-phiX174	2470	2480	737769.23
-phiX174	2480	2490	753807.69
-phiX174	2490	2500	769846.15
-phiX174	2500	2510	785884.62
-phiX174	2510	2520	641538.46
-phiX174	2520	2530	657576.92
-phiX174	2530	2540	529269.23
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-phiX174	2870	2880	705692.31
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diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCoverage_result4.bw
Binary file test-data/bamCoverage_result4.bw has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamCoverage_result5.bw
Binary file test-data/bamCoverage_result5.bw has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamPEFragmentSize_histogram_result1.png
Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt	Fri May 13 17:13:52 2016 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt	Thu Aug 11 06:28:53 2016 -0400
@@ -1,6 +1,8 @@
+
+
+BAM file : 0.bam
 Sample size: 3
 
-
 Fragment lengths:
 Min.: 241.0
 1st Qu.: 241.5
diff -r eab93a5553ec -r 96057da0d8d8 test-data/correctGCBias_result1.bam
Binary file test-data/correctGCBias_result1.bam has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/plotEnrichment_output.png
Binary file test-data/plotEnrichment_output.png has changed
diff -r eab93a5553ec -r 96057da0d8d8 test-data/plotEnrichment_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotEnrichment_output.txt	Thu Aug 11 06:28:53 2016 -0400
@@ -0,0 +1,5 @@
+file	featureType	percent
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+bowtie2 test1.bam	up	100.00
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diff -r eab93a5553ec -r 96057da0d8d8 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular	Fri May 13 17:13:52 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Thu Aug 11 06:28:53 2016 -0400
@@ -1,239 +1,239 @@
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