Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

changeset 10:2a56d1eb6c46 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 08:05:47 -0500
parents 4efe24a9739e
children 82c669810520
files 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 17 files changed, 846 insertions(+), 771 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Tue Oct 25 19:03:45 2016 -0400
+++ b/deepTools_macros.xml	Mon Dec 05 08:05:47 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 19:03:45 2016 -0400
+++ b/test-data/bamCompare_result1.bg	Mon Dec 05 08:05:47 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 19:03:45 2016 -0400
+++ b/test-data/bamCoverage_result3.bg	Mon Dec 05 08:05:47 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 19:03:45 2016 -0400
+++ b/test-data/bamCoverage_result4.bg	Mon Dec 05 08:05:47 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
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-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
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-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
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-phiX174	2180	2190	440176.46
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-phiX174	2210	2220	489084.95
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-phiX174	2230	2240	603204.78
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-phiX174	3190	3200	668416.10
-phiX174	3200	3210	684718.93
-phiX174	3210	3220	749930.26
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--- a/test-data/bigwigCompare_result2.bg	Tue Oct 25 19:03:45 2016 -0400
+++ b/test-data/bigwigCompare_result2.bg	Mon Dec 05 08:05:47 2016 -0500
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--- a/test-data/computeGCBias_result1.tabular	Tue Oct 25 19:03:45 2016 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrixOperations.txt	Mon Dec 05 08:05:47 2016 -0500
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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 19:03:45 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Mon Dec 05 08:05:47 2016 -0500
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Binary file test-data/sequence.2bit has changed
--- a/tool_dependencies.xml	Tue Oct 25 19:03:45 2016 -0400
+++ b/tool_dependencies.xml	Mon Dec 05 08:05:47 2016 -0500
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-    <package name="deepTools" version="2.3.6">
-        <repository changeset_revision="05f46fef1ea5" name="package_python_2_7_deeptools_2_3_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="deeptools" version="2.4.1">
+        <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>