Mercurial > repos > bgruening > deeptools_plot_correlation

changeset 8:162837c86cbc draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Tue, 20 Sep 2016 03:03:14 -0400
parents b3589208f673
children cdde99ce71c8
files deepTools_macros.xml static/images/plotEnrichment_output.png test-data/bamCompare_result1.bg test-data/bamCoverage_result1.bw 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/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_result1.txt test-data/correctGCBias_result1.bam test-data/plotEnrichment_output.png test-data/plotEnrichment_output.txt test-data/plotFingerprint_result2.tabular tool_dependencies.xml
diffstat 16 files changed, 828 insertions(+), 722 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Fri May 13 14:24:25 2016 -0400
+++ b/deepTools_macros.xml	Tue Sep 20 03:03:14 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>
 
@@ -72,18 +91,18 @@
             <sanitizer>
                 <valid initial="string.letters,string.digits">
                     <add value="|"/>
+                    <add value=":"/>
                  </valid>
             </sanitizer>
         </param>
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.2.3</token>
+    <token name="@WRAPPER_VERSION@">2.3.5</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.2.3">deepTools</requirement>
+            <requirement type="package" version="2.3.5">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -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>
Binary file static/images/plotEnrichment_output.png has changed
--- a/test-data/bamCompare_result1.bg	Fri May 13 14:24:25 2016 -0400
+++ b/test-data/bamCompare_result1.bg	Tue Sep 20 03:03:14 2016 -0400
@@ -1,1 +1,1 @@
-chrM	0	16569	1.0
+chrM	0	16569	1.00
Binary file test-data/bamCoverage_result1.bw has changed
Binary file test-data/bamCoverage_result2.bw has changed
--- a/test-data/bamCoverage_result3.bg	Fri May 13 14:24:25 2016 -0400
+++ b/test-data/bamCoverage_result3.bg	Tue Sep 20 03:03:14 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
--- a/test-data/bamCoverage_result4.bg	Fri May 13 14:24:25 2016 -0400
+++ b/test-data/bamCoverage_result4.bg	Tue Sep 20 03:03:14 2016 -0400
@@ -1,472 +1,472 @@
-phiX174	0	10	16038.46
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-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
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-phiX174	320	330	368884.62
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-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
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-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
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-phiX174	870	880	256615.38
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-phiX174	910	920	545307.69
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-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
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-phiX174	1090	1100	769846.15
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-phiX174	1110	1120	657576.92
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-phiX174	1130	1140	625500.00
-phiX174	1140	1150	673615.38
-phiX174	1150	1160	625500.00
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-phiX174	1170	1180	609461.54
-phiX174	1180	1190	577384.62
-phiX174	1190	1200	513230.77
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-phiX174	1210	1220	561346.15
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-phiX174	1270	1280	352846.15
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-phiX174	1290	1300	320769.23
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-phiX174	2000	2010	673615.38
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-phiX174	2800	2810	834000.00
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-phiX174	2820	2830	673615.38
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-phiX174	2840	2860	625500.00
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-phiX174	2870	2880	705692.31
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-phiX174	2890	2900	609461.54
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-phiX174	2930	2940	513230.77
-phiX174	2940	2950	561346.15
-phiX174	2950	2960	497192.31
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-phiX174	2990	3000	529269.23
-phiX174	3000	3010	561346.15
-phiX174	3010	3020	513230.77
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-phiX174	3040	3050	417000.00
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-phiX174	3060	3070	561346.15
-phiX174	3070	3080	625500.00
-phiX174	3080	3100	577384.62
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-phiX174	3200	3210	673615.38
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-phiX174	3220	3230	657576.92
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-phiX174	3240	3250	625500.00
-phiX174	3250	3260	545307.69
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-phiX174	3270	3280	625500.00
-phiX174	3280	3290	577384.62
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-phiX174	3300	3310	513230.77
-phiX174	3310	3320	529269.23
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-phiX174	3430	3440	513230.77
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-phiX174	3490	3500	834000.00
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-phiX174	3510	3520	898153.85
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-phiX174	3530	3540	753807.69
-phiX174	3540	3550	785884.62
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-phiX174	3560	3570	689653.85
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-phiX174	3610	3620	417000.00
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-phiX174	3660	3680	400961.54
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-phiX174	3990	4000	641538.46
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Binary file test-data/bamCoverage_result4.bw has changed
Binary file test-data/bamCoverage_result5.bw has changed
Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed
--- a/test-data/bamPEFragmentSize_result1.txt	Fri May 13 14:24:25 2016 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt	Tue Sep 20 03:03:14 2016 -0400
@@ -1,6 +1,8 @@
+
+
+BAM file : 0.bam
 Sample size: 3
 
-
 Fragment lengths:
 Min.: 241.0
 1st Qu.: 241.5
Binary file test-data/correctGCBias_result1.bam has changed
Binary file test-data/plotEnrichment_output.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotEnrichment_output.txt	Tue Sep 20 03:03:14 2016 -0400
@@ -0,0 +1,5 @@
+file	featureType	percent
+bowtie2 test1.bam	down	100.00
+bowtie2 test1.bam	up	100.00
+bowtie2 test1.bam	down	100.00
+bowtie2 test1.bam	up	100.00
--- a/test-data/plotFingerprint_result2.tabular	Fri May 13 14:24:25 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular	Tue Sep 20 03:03:14 2016 -0400
@@ -1,239 +1,239 @@
 'bowtie2 test1.bam'	'bowtie2 test1.bam'
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--- a/tool_dependencies.xml	Fri May 13 14:24:25 2016 -0400
+++ b/tool_dependencies.xml	Tue Sep 20 03:03:14 2016 -0400
@@ -3,7 +3,7 @@
     <package name="python" version="2.7.10">
         <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
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-        <repository changeset_revision="2f4601e4fc32" name="package_python_2_7_deeptools_2_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="deepTools" version="2.3.5">
+        <repository changeset_revision="c3e87c8140fe" name="package_python_2_7_deeptools_2_3_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>