Mercurial > repos > bgruening > deeptools_bam_coverage

changeset 25:bc24fb3f9e91 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 07:49:48 -0500
parents 01f5d767c869
children 651432fd3139
files bamCoverage.xml deepTools_macros.xml test-data/bamCompare_result1.bg test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/bamCoverage_result4.bg test-data/bamCoverage_result4.bw test-data/bamCoverage_result5.bw test-data/bamCoverage_result6.bw test-data/bigwigCompare_result2.bg test-data/computeGCBias_result1.tabular test-data/computeMatrixOperations.txt test-data/computeMatrixOperations_result2.mat.gz test-data/correctGCBias_result1.bam test-data/plotFingerprint_quality_metrics.tabular test-data/plotFingerprint_result2.tabular test-data/sequence.2bit tool_dependencies.xml
diffstat 18 files changed, 863 insertions(+), 775 deletions(-) [+]
line wrap: on
line diff
--- a/bamCoverage.xml	Tue Oct 25 18:27:46 2016 -0400
+++ b/bamCoverage.xml	Mon Dec 05 07:49:48 2016 -0500
@@ -52,7 +52,7 @@
                 #end if
 
                 #if $advancedOpt.Offset:
-                    --Offset '$advancedOpt.Offset'
+                    --Offset $advancedOpt.Offset
                 #end if
 
                 @blacklist@
@@ -115,7 +115,7 @@
                     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. 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"
+                <param argument="--Offset" type="text"  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
@@ -124,8 +124,10 @@
                         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." />
+                        offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
+                        used to specify a range of positions. Note that specifying something like
+                        --Offset 5 -1 will result in the 5th through last position being used, which
+                        is equivalent to trimming 4 bases from the 5-prime end of alignments." />
 
                 <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.
@@ -192,6 +194,17 @@
             <param name="binSize" value="10" />
             <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
         </test>
+        <test>
+            <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="binSize" value="10" />
+            <param name="Offset" value="-4 -1" />
+            <param name="doExtend" value="yes" />
+            <param name="minMappingQuality" value="0" />
+            <param name="type" value="no" />
+            <output name="outFileName" file="bamCoverage_result6.bw" ftype="bigwig" />
+        </test>
     </tests>
     <help>
 <![CDATA[
--- a/deepTools_macros.xml	Tue Oct 25 18:27:46 2016 -0400
+++ b/deepTools_macros.xml	Mon Dec 05 07:49:48 2016 -0500
@@ -98,11 +98,11 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.3.6</token>
+    <token name="@WRAPPER_VERSION@">2.4.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="package" version="2.3.6">deepTools</requirement>
+            <requirement type="package" version="2.4.1">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -285,11 +285,21 @@
         </param>
     </xml>
 
+    <xml name="sortRegionsComputeMatrix">
+        <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="keep" selected="true">maintain the same ordering as the input files</option>
+            <option value="descend">descending order</option>
+            <option value="ascend">ascending order</option>
+        </param>
+    </xml>
+
     <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="descend" selected="true">descending order</option>
+            <option value="descend">descending order</option>
             <option value="ascend">ascending order</option>
         </param>
     </xml>
@@ -362,21 +372,62 @@
     </xml>
 
     <xml name="multiple_input_bams">
-        <param argument="--bamfiles" type="data" format="bam" min="1"
-            label="Bam file" multiple="true"
-            help=""/>
+        <conditional name="multibam_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 is vital to you, select Yes below.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <when value="No">
+            <param argument="--bamfiles" type="data" format="bam" min="1"
+                label="Bam file" multiple="true"
+                help=""/>
+        </when>
+        <when value="Yes">
+            <repeat name="multibam_repeats" min="1" title="BAM Files">
+                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
+            </repeat>
+        </when>
+        </conditional>
     </xml>
 
     <xml name="multiple_input_bams_min2">
-        <param argument="--bamfiles" type="data" format="bam" min="2"
-            label="Bam file" multiple="true"
-            help=""/>
+        <conditional name="multibam_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 
+is vital to you, select Yes below.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <when value="No">
+            <param argument="--bamfiles" type="data" format="bam" min="2"
+                label="Bam file" multiple="true"
+                help=""/>
+        </when>
+        <when value="Yes">
+            <repeat name="multibam_repeats" min="2" title="BAM Files">
+                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
+            </repeat>
+        </when>
+        </conditional>
     </xml>
 
     <xml name="multiple_input_bigwigs">
-        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
-            label="Bigwig file"
-            help="A Bigwig file."/>
+        <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 
+is vital to you, select Yes below.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <when value="No">
+            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
+                label="Bigwig file"
+                help="A Bigwig file."/>
+        </when>
+        <when value="Yes">
+            <repeat name="multibigwig_repeats" min="2" title="BigWig files">
+                <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
+            </repeat>
+        </when>
+        </conditional>
     </xml>
 
     <xml name="plotTitle">
@@ -390,12 +441,21 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
-        #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
+        #if $multibam_conditional.orderMatters == "No":
+            #for $counter, $bamfile in enumerate($multibam_conditional.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
+        #else:
+            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
+                ln -s "${f.bamfile}" "./${counter}.bam" &&
+                ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+                #silent $files.append('%s.bam' % $counter)
+                #silent $labels.append("'%s'" % ($f.bamfile.display_name))
+            #end for
+        #end if
 ]]>
     </token>
 
@@ -403,11 +463,19 @@
 <![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
+        #if $multibigwig_conditional.orderMatters == "No":
+            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
+                ln -s "${bigwig}" "${counter}.bw" &&
+                #silent $files.append('%s.bw' % $counter)
+                #silent $labels.append("'%s'" % ($bigwig.display_name))
+            #end for
+        #else:
+            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
+                ln -s "${f.bigwig}" "${counter}.bw" &&
+                #silent $files.append('%s.bw' % $counter)
+                #silent $labels.append("'%s'" % ($f.bigwig.display_name))
+            #end for
+        #end if
 ]]>
     </token>
 
--- a/test-data/bamCompare_result1.bg	Tue Oct 25 18:27:46 2016 -0400
+++ b/test-data/bamCompare_result1.bg	Mon Dec 05 07:49:48 2016 -0500
@@ -1,1 +1,1 @@
-chrM	0	16569	1.00
+chrM	0	16569	1
Binary file test-data/bamCoverage_result2.bw has changed
--- a/test-data/bamCoverage_result3.bg	Tue Oct 25 18:27:46 2016 -0400
+++ b/test-data/bamCoverage_result3.bg	Mon Dec 05 07:49:48 2016 -0500
@@ -1,7 +1,7 @@
-chrM	0	210	9768764.94
-chrM	210	220	9560918.88
-chrM	220	230	7690304.31
-chrM	230	240	5196151.56
-chrM	240	250	3325537.00
-chrM	250	260	623538.19
-chrM	260	16569	0.00
+chrM	0	210	9.76876e+06
+chrM	210	220	9.56092e+06
+chrM	220	230	7.6903e+06
+chrM	230	240	5.19615e+06
+chrM	240	250	3.32554e+06
+chrM	250	260	623538
+chrM	260	16569	0
--- a/test-data/bamCoverage_result4.bg	Tue Oct 25 18:27:46 2016 -0400
+++ b/test-data/bamCoverage_result4.bg	Mon Dec 05 07:49:48 2016 -0500
@@ -1,472 +1,472 @@
-phiX174	0	10	16302.83
-phiX174	10	20	48908.50
-phiX174	20	70	146725.49
-phiX174	70	80	195633.98
-phiX174	80	90	179331.15
-phiX174	90	100	163028.32
-phiX174	100	120	114119.82
-phiX174	120	140	146725.49
-phiX174	140	150	163028.32
-phiX174	150	160	130422.65
-phiX174	160	170	163028.32
-phiX174	170	180	179331.15
-phiX174	180	200	211936.81
-phiX174	200	210	195633.98
-phiX174	210	220	244542.48
-phiX174	220	230	277148.14
-phiX174	230	240	342359.47
-phiX174	240	250	326056.64
-phiX174	250	260	293450.97
-phiX174	260	270	342359.47
-phiX174	270	280	407570.79
-phiX174	280	300	423873.63
-phiX174	300	310	358662.30
-phiX174	310	320	326056.64
-phiX174	320	330	374965.13
-phiX174	330	340	358662.30
-phiX174	340	350	293450.97
-phiX174	350	360	260845.31
-phiX174	360	370	228239.64
-phiX174	370	380	244542.48
-phiX174	380	390	309753.80
-phiX174	390	400	260845.31
-phiX174	400	410	244542.48
-phiX174	410	420	228239.64
-phiX174	420	450	293450.97
-phiX174	450	460	309753.80
-phiX174	460	470	342359.47
-phiX174	470	490	423873.63
-phiX174	490	510	505387.79
-phiX174	510	520	472782.12
-phiX174	520	530	570599.11
-phiX174	530	540	505387.79
-phiX174	540	550	537993.45
-phiX174	550	560	554296.28
-phiX174	560	570	652113.27
-phiX174	570	580	635810.44
-phiX174	580	590	570599.11
-phiX174	590	600	619507.61
-phiX174	600	610	554296.28
-phiX174	610	630	635810.44
-phiX174	630	640	586901.94
-phiX174	640	650	521690.62
-phiX174	650	660	554296.28
-phiX174	660	670	570599.11
-phiX174	670	680	603204.78
-phiX174	680	690	668416.10
-phiX174	690	700	652113.27
-phiX174	700	710	570599.11
-phiX174	710	730	603204.78
-phiX174	730	740	521690.62
-phiX174	740	760	603204.78
-phiX174	760	770	505387.79
-phiX174	770	780	521690.62
-phiX174	780	790	537993.45
-phiX174	790	800	554296.28
-phiX174	800	810	456479.29
-phiX174	810	820	440176.46
-phiX174	820	830	374965.13
-phiX174	830	840	326056.64
-phiX174	840	850	358662.30
-phiX174	850	860	309753.80
-phiX174	860	870	342359.47
-phiX174	870	880	260845.31
-phiX174	880	890	358662.30
-phiX174	890	900	391267.96
-phiX174	900	910	472782.12
-phiX174	910	920	554296.28
-phiX174	920	930	570599.11
-phiX174	930	940	554296.28
-phiX174	940	950	586901.94
-phiX174	950	960	603204.78
-phiX174	960	970	521690.62
-phiX174	970	980	489084.95
-phiX174	980	990	440176.46
-phiX174	990	1000	423873.63
-phiX174	1000	1010	456479.29
-phiX174	1010	1030	586901.94
-phiX174	1030	1040	766233.09
-phiX174	1040	1050	798838.76
-phiX174	1050	1060	831444.42
-phiX174	1060	1070	880352.92
-phiX174	1070	1080	847747.25
-phiX174	1080	1090	880352.92
-phiX174	1090	1100	782535.93
-phiX174	1100	1110	749930.26
-phiX174	1110	1120	668416.10
-phiX174	1120	1130	652113.27
-phiX174	1130	1140	635810.44
-phiX174	1140	1150	684718.93
-phiX174	1150	1160	635810.44
-phiX174	1160	1170	603204.78
-phiX174	1170	1180	619507.61
-phiX174	1180	1190	586901.94
-phiX174	1190	1200	521690.62
-phiX174	1200	1210	489084.95
-phiX174	1210	1220	570599.11
-phiX174	1220	1230	489084.95
-phiX174	1230	1240	456479.29
-phiX174	1240	1250	358662.30
-phiX174	1250	1260	342359.47
-phiX174	1260	1270	407570.79
-phiX174	1270	1280	358662.30
-phiX174	1280	1290	374965.13
-phiX174	1290	1300	326056.64
-phiX174	1300	1310	391267.96
-phiX174	1310	1320	521690.62
-phiX174	1320	1330	505387.79
-phiX174	1330	1340	521690.62
-phiX174	1340	1350	489084.95
-phiX174	1350	1370	505387.79
-phiX174	1370	1390	472782.12
-phiX174	1390	1400	358662.30
-phiX174	1400	1410	456479.29
-phiX174	1410	1430	489084.95
-phiX174	1430	1450	554296.28
-phiX174	1450	1460	570599.11
-phiX174	1460	1470	586901.94
-phiX174	1470	1480	619507.61
-phiX174	1480	1490	603204.78
-phiX174	1490	1500	554296.28
-phiX174	1500	1510	668416.10
-phiX174	1510	1520	635810.44
-phiX174	1520	1540	798838.76
-phiX174	1540	1550	733627.43
-phiX174	1550	1570	766233.09
-phiX174	1570	1580	782535.93
-phiX174	1580	1590	684718.93
-phiX174	1590	1600	635810.44
-phiX174	1600	1610	570599.11
-phiX174	1610	1620	537993.45
-phiX174	1620	1630	505387.79
-phiX174	1630	1640	472782.12
-phiX174	1640	1650	489084.95
-phiX174	1650	1660	505387.79
-phiX174	1660	1670	537993.45
-phiX174	1670	1680	603204.78
-phiX174	1680	1690	521690.62
-phiX174	1690	1700	537993.45
-phiX174	1700	1710	603204.78
-phiX174	1710	1720	554296.28
-phiX174	1720	1730	537993.45
-phiX174	1730	1740	586901.94
-phiX174	1740	1750	537993.45
-phiX174	1750	1760	440176.46
-phiX174	1760	1770	423873.63
-phiX174	1770	1780	374965.13
-phiX174	1780	1790	358662.30
-phiX174	1790	1810	342359.47
-phiX174	1810	1820	326056.64
-phiX174	1820	1830	472782.12
-phiX174	1830	1860	717324.60
-phiX174	1860	1870	815141.59
-phiX174	1870	1880	749930.26
-phiX174	1880	1890	684718.93
-phiX174	1890	1900	717324.60
-phiX174	1900	1910	619507.61
-phiX174	1910	1920	407570.79
-phiX174	1920	1930	472782.12
-phiX174	1930	1940	554296.28
-phiX174	1940	1950	456479.29
-phiX174	1950	1960	489084.95
-phiX174	1960	1970	537993.45
-phiX174	1970	1980	684718.93
-phiX174	1980	1990	652113.27
-phiX174	1990	2000	668416.10
-phiX174	2000	2010	684718.93
-phiX174	2010	2020	652113.27
-phiX174	2020	2030	668416.10
-phiX174	2030	2050	684718.93
-phiX174	2050	2060	489084.95
-phiX174	2060	2070	521690.62
-phiX174	2070	2080	489084.95
-phiX174	2080	2100	521690.62
-phiX174	2100	2110	537993.45
-phiX174	2110	2120	521690.62
-phiX174	2120	2130	537993.45
-phiX174	2130	2140	554296.28
-phiX174	2140	2150	521690.62
-phiX174	2150	2160	554296.28
-phiX174	2160	2170	423873.63
-phiX174	2170	2180	358662.30
-phiX174	2180	2190	440176.46
-phiX174	2190	2200	456479.29
-phiX174	2200	2210	440176.46
-phiX174	2210	2220	489084.95
-phiX174	2220	2230	554296.28
-phiX174	2230	2240	603204.78
-phiX174	2240	2250	635810.44
-phiX174	2250	2260	733627.43
-phiX174	2260	2270	635810.44
-phiX174	2270	2290	603204.78
-phiX174	2290	2300	619507.61
-phiX174	2300	2310	749930.26
-phiX174	2310	2320	782535.93
-phiX174	2320	2330	880352.92
-phiX174	2330	2340	864050.08
-phiX174	2340	2350	912958.58
-phiX174	2350	2360	815141.59
-phiX174	2360	2370	929261.41
-phiX174	2370	2380	815141.59
-phiX174	2380	2390	652113.27
-phiX174	2390	2400	603204.78
-phiX174	2400	2410	423873.63
-phiX174	2410	2420	407570.79
-phiX174	2420	2430	358662.30
-phiX174	2430	2440	489084.95
-phiX174	2440	2450	456479.29
-phiX174	2450	2460	619507.61
-phiX174	2460	2470	684718.93
-phiX174	2470	2480	749930.26
-phiX174	2480	2490	766233.09
-phiX174	2490	2500	782535.93
-phiX174	2500	2510	798838.76
-phiX174	2510	2520	652113.27
-phiX174	2520	2530	668416.10
-phiX174	2530	2540	537993.45
-phiX174	2540	2550	472782.12
-phiX174	2550	2560	391267.96
-phiX174	2560	2570	440176.46
-phiX174	2570	2590	472782.12
-phiX174	2590	2600	456479.29
-phiX174	2600	2620	537993.45
-phiX174	2620	2630	554296.28
-phiX174	2630	2640	701021.77
-phiX174	2640	2650	635810.44
-phiX174	2650	2660	570599.11
-phiX174	2660	2670	554296.28
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--- a/test-data/bigwigCompare_result2.bg	Tue Oct 25 18:27:46 2016 -0400
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--- a/test-data/computeGCBias_result1.tabular	Tue Oct 25 18:27:46 2016 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/test-data/plotFingerprint_result2.tabular	Tue Oct 25 18:27:46 2016 -0400
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Binary file test-data/sequence.2bit has changed
--- a/tool_dependencies.xml	Tue Oct 25 18:27:46 2016 -0400
+++ b/tool_dependencies.xml	Mon Dec 05 07:49:48 2016 -0500
@@ -3,7 +3,7 @@
     <package name="python" version="2.7.10">
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deepTools" version="2.3.6">
-        <repository changeset_revision="c8a81f75545e" name="package_python_2_7_deeptools_2_3_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="deeptools" version="2.4.1">
+        <repository changeset_revision="939327bd44e7" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>