Repository 'deeptools_compute_matrix'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix

Changeset 8:aee77c22123d (2016-09-20)
Previous changeset 7:17d456f4051b (2016-05-13) Next changeset 9:4b3adcb7c7e9 (2016-10-25)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
modified:
computeMatrix.xml
deepTools_macros.xml
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/plotFingerprint_result2.tabular
tool_dependencies.xml
added:
static/images/plotEnrichment_output.png
test-data/plotEnrichment_output.png
test-data/plotEnrichment_output.txt
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diff -r 17d456f4051b -r aee77c22123d computeMatrix.xml
--- a/computeMatrix.xml Fri May 13 14:38:45 2016 -0400
+++ b/computeMatrix.xml Tue Sep 20 03:07:09 2016 -0400
b
@@ -76,6 +76,11 @@
                 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
+
+                @ADVANCED_OPTS_GTF@
+
+                @blacklist@
+
             #end if
 ]]>
     </command>
@@ -206,6 +211,10 @@
                     bias the average values. (--maxThreshold)"/>
                 <param name="scale" type="float" optional="True" label="Scaling factor"
                     help="If set, all values are multiplied by this number. (--scale)"/>
+
+                <expand macro="gtf_options" />
+
+                <expand macro="blacklist" />
             </when>
         </conditional>
     </inputs>
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diff -r 17d456f4051b -r aee77c22123d deepTools_macros.xml
--- a/deepTools_macros.xml Fri May 13 14:38:45 2016 -0400
+++ b/deepTools_macros.xml Tue Sep 20 03:07:09 2016 -0400
[
b'@@ -30,6 +30,25 @@\n         #if $advancedOpt.samFlagExclude:\n             --samFlagExclude $advancedOpt.samFlagExclude\n         #end if\n+        #if $advancedOpt.minFragmentLength:\n+            --minFragmentLength $advancedOpt.minFragmentLength\n+        #end if\n+        #if $advancedOpt.maxFragmentLength:\n+            --maxFragmentLength $advancedOpt.maxFragmentLength\n+        #end if\n+    </token>\n+\n+    <token name="@ADVANCED_OPTS_GTF@">\n+        $advancedOpt.metagene\n+        #if $advancedOpt.transcriptID:\n+            --transcriptID $advancedOpt.transcriptID\n+        #end if\n+        #if $advancedOpt.exonID:\n+            --exonID $advancedOpt.exonID\n+        #end if\n+        #if $advancedOpt.transcript_id_designator:\n+            --transcript_id_designator $advancedOpt.transcript_id_designator\n+        #end if\n     </token>\n \n     <xml name="heatmap_options">\n@@ -59,9 +78,9 @@\n     </xml>\n \n     <xml name="zMin_zMax">\n-        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+        <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"\n             help="If not specified the value is set automatically."/>\n-        <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+        <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"\n             help="If not specified the value is set automatically."/>\n     </xml>\n \n@@ -72,18 +91,18 @@\n             <sanitizer>\n                 <valid initial="string.letters,string.digits">\n                     <add value="|"/>\n+                    <add value=":"/>\n                  </valid>\n             </sanitizer>\n         </param>\n     </xml>\n \n     <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n-    <token name="@WRAPPER_VERSION@">2.2.3</token>\n+    <token name="@WRAPPER_VERSION@">2.3.5</token>\n     <xml name="requirements">\n         <requirements>\n             <requirement type="package" version="2.7.10">python</requirement>\n-            <requirement type="binary">@BINARY@</requirement>\n-            <requirement type="package" version="2.2.3">deepTools</requirement>\n+            <requirement type="package" version="2.3.5">deepTools</requirement>\n             <yield />\n         </requirements>\n         <expand macro="stdio" />\n@@ -159,14 +178,43 @@\n             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."/>\n     </xml>\n \n+    <xml name="fragLength">\n+        <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"\n+            label="Minimum fragment length for inclusion."\n+            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." />\n+        <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"\n+            label="Maximum fragment length for inclusion."\n+            help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />\n+    </xml>\n+\n     <xml name="read_processing_options">\n         <expand macro="extendReads" />\n         <expand macro="ignoreDuplicates" />\n         <expand macro="centerReads" />\n         <expand macro="minMappingQuality" />\n         <expand macro="samFlags" />\n+        <expand macro="fragLength" />\n     </xml>\n \n+    <xml name="gtf_options">\n+        <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""\n+            label="Use a metagene model"\n+            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 mRN'..b'D/GTF format"\n+            help="One or more files containing regions to exclude from the analysis" />\n+    </xml>\n+\n+    <token name="@blacklist@">\n+<![CDATA[\n+        #if \' \'.join( map(str, $advancedOpt.blackListFileName) ) != \'None\':\n+            #set blfiles=[]\n+            #for $f in $advancedOpt.blackListFileName:\n+                #silent $blfiles.append("\'%s\'" % $f)\n+            #end for\n+            #if $blfiles != ["\'None\'"]:\n+                --blackListFileName #echo \' \'.join($blfiles)#\n+            #end if\n+        #end if\n+]]> \n+    </token>\n+\n+    <xml name="multiple_bed">\n+        <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"\n+            label="Regions in BED/GTF format"\n+            help="One or more files containing regions to include in the analysis" />\n+    </xml>\n+\n+    <token name="@multiple_bed@">\n+<![CDATA[\n+        #set files=[]\n+        #set labels=[]\n+        #for $f in $BED:\n+            #silent $files.append("\'%s\'" % $f)\n+            #silent $labels.append("\'%s\'" % $f.display_name)\n+        #end for\n+        #if len($files) > 0:\n+            --BED #echo \' \'.join($files)#\n+            --regionLabels #echo \' \'.join($labels)#\n+        #end if\n+]]> \n+    </token>\n+\n     <xml name="reference_genome_source">\n         <conditional name="source">\n             <param name="ref_source" type="select" label="Reference genome">\n@@ -404,7 +493,8 @@\n                 <option value="specific">user specified</option>\n             </param>\n             <when value="specific">\n-                <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n+                <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"\n+                       help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n             </when>\n             <when value="2150570000" />\n             <when value="2451960000" />\n@@ -439,7 +529,10 @@\n             <when value="no" />\n             <when value="yes">\n                 <yield />\n-                <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."/>\n+                <param name="saveSortedRegions" type="boolean"\n+                       label="Save the regions after skipping zeros or min/max threshold values"\n+                       help="The order of the regions in the file follows the sorting order selected. This is useful,\n+                       for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n             </when>\n         </conditional>\n     </xml>\n@@ -454,6 +547,11 @@\n         </param>\n     </xml>\n \n+    <xml name="output_dpi">\n+        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"\n+            label="Image dpi" help=""/>\n+    </xml>\n+\n     <xml name="output_image_file_format">\n         <data format="png" name="outFileName" label="${tool.name} image">\n             <change_format>\n@@ -497,7 +595,9 @@\n     </xml>\n \n     <xml name="colorMap">\n-        <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">\n+        <param name="colorMap" type="select" label="Color map to use for the heatmap"\n+               help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"\n+               multiple="true">\n             <option value="RdYlBu" selected="true">RdYlBu</option>\n             <option value="Accent">Accent</option>\n             <option value="Spectral">Spectral</option>\n'
b
diff -r 17d456f4051b -r aee77c22123d static/images/plotEnrichment_output.png
b
Binary file static/images/plotEnrichment_output.png has changed
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diff -r 17d456f4051b -r aee77c22123d test-data/bamCompare_result1.bg
--- a/test-data/bamCompare_result1.bg Fri May 13 14:38:45 2016 -0400
+++ b/test-data/bamCompare_result1.bg Tue Sep 20 03:07:09 2016 -0400
b
@@ -1,1 +1,1 @@
-chrM 0 16569 1.0
+chrM 0 16569 1.00
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diff -r 17d456f4051b -r aee77c22123d test-data/bamCoverage_result1.bw
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Binary file test-data/bamCoverage_result1.bw has changed
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diff -r 17d456f4051b -r aee77c22123d test-data/bamCoverage_result2.bw
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Binary file test-data/bamCoverage_result2.bw has changed
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diff -r 17d456f4051b -r aee77c22123d test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg Fri May 13 14:38:45 2016 -0400
+++ b/test-data/bamCoverage_result3.bg Tue Sep 20 03:07:09 2016 -0400
b
@@ -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
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diff -r 17d456f4051b -r aee77c22123d test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg Fri May 13 14:38:45 2016 -0400
+++ b/test-data/bamCoverage_result4.bg Tue Sep 20 03:07:09 2016 -0400
b
b'@@ -1,472 +1,472 @@\n-phiX174\t0\t10\t16038.46\n-phiX174\t10\t20\t48115.38\n-phiX174\t20\t70\t144346.15\n-phiX174\t70\t80\t192461.54\n-phiX174\t80\t90\t176423.08\n-phiX174\t90\t100\t160384.62\n-phiX174\t100\t120\t112269.23\n-phiX174\t120\t140\t144346.15\n-phiX174\t140\t150\t160384.62\n-phiX174\t150\t160\t128307.69\n-phiX174\t160\t170\t160384.62\n-phiX174\t170\t180\t176423.08\n-phiX174\t180\t200\t208500.00\n-phiX174\t200\t210\t192461.54\n-phiX174\t210\t220\t240576.92\n-phiX174\t220\t230\t272653.85\n-phiX174\t230\t240\t336807.69\n-phiX174\t240\t250\t320769.23\n-phiX174\t250\t260\t288692.31\n-phiX174\t260\t270\t336807.69\n-phiX174\t270\t280\t400961.54\n-phiX174\t280\t300\t417000.00\n-phiX174\t300\t310\t352846.15\n-phiX174\t310\t320\t320769.23\n-phiX174\t320\t330\t368884.62\n-phiX174\t330\t340\t352846.15\n-phiX174\t340\t350\t288692.31\n-phiX174\t350\t360\t256615.38\n-phiX174\t360\t370\t224538.46\n-phiX174\t370\t380\t240576.92\n-phiX174\t380\t390\t304730.77\n-phiX174\t390\t400\t256615.38\n-phiX174\t400\t410\t240576.92\n-phiX174\t410\t420\t224538.46\n-phiX174\t420\t450\t288692.31\n-phiX174\t450\t460\t304730.77\n-phiX174\t460\t470\t336807.69\n-phiX174\t470\t490\t417000.00\n-phiX174\t490\t510\t497192.31\n-phiX174\t510\t520\t465115.38\n-phiX174\t520\t530\t561346.15\n-phiX174\t530\t540\t497192.31\n-phiX174\t540\t550\t529269.23\n-phiX174\t550\t560\t545307.69\n-phiX174\t560\t570\t641538.46\n-phiX174\t570\t580\t625500.00\n-phiX174\t580\t590\t561346.15\n-phiX174\t590\t600\t609461.54\n-phiX174\t600\t610\t545307.69\n-phiX174\t610\t630\t625500.00\n-phiX174\t630\t640\t577384.62\n-phiX174\t640\t650\t513230.77\n-phiX174\t650\t660\t545307.69\n-phiX174\t660\t670\t561346.15\n-phiX174\t670\t680\t593423.08\n-phiX174\t680\t690\t657576.92\n-phiX174\t690\t700\t641538.46\n-phiX174\t700\t710\t561346.15\n-phiX174\t710\t730\t593423.08\n-phiX174\t730\t740\t513230.77\n-phiX174\t740\t760\t593423.08\n-phiX174\t760\t770\t497192.31\n-phiX174\t770\t780\t513230.77\n-phiX174\t780\t790\t529269.23\n-phiX174\t790\t800\t545307.69\n-phiX174\t800\t810\t449076.92\n-phiX174\t810\t820\t433038.46\n-phiX174\t820\t830\t368884.62\n-phiX174\t830\t840\t320769.23\n-phiX174\t840\t850\t352846.15\n-phiX174\t850\t860\t304730.77\n-phiX174\t860\t870\t336807.69\n-phiX174\t870\t880\t256615.38\n-phiX174\t880\t890\t352846.15\n-phiX174\t890\t900\t384923.08\n-phiX174\t900\t910\t465115.38\n-phiX174\t910\t920\t545307.69\n-phiX174\t920\t930\t561346.15\n-phiX174\t930\t940\t545307.69\n-phiX174\t940\t950\t577384.62\n-phiX174\t950\t960\t593423.08\n-phiX174\t960\t970\t513230.77\n-phiX174\t970\t980\t481153.85\n-phiX174\t980\t990\t433038.46\n-phiX174\t990\t1000\t417000.00\n-phiX174\t1000\t1010\t449076.92\n-phiX174\t1010\t1030\t577384.62\n-phiX174\t1030\t1040\t753807.69\n-phiX174\t1040\t1050\t785884.62\n-phiX174\t1050\t1060\t817961.54\n-phiX174\t1060\t1070\t866076.92\n-phiX174\t1070\t1080\t834000.00\n-phiX174\t1080\t1090\t866076.92\n-phiX174\t1090\t1100\t769846.15\n-phiX174\t1100\t1110\t737769.23\n-phiX174\t1110\t1120\t657576.92\n-phiX174\t1120\t1130\t641538.46\n-phiX174\t1130\t1140\t625500.00\n-phiX174\t1140\t1150\t673615.38\n-phiX174\t1150\t1160\t625500.00\n-phiX174\t1160\t1170\t593423.08\n-phiX174\t1170\t1180\t609461.54\n-phiX174\t1180\t1190\t577384.62\n-phiX174\t1190\t1200\t513230.77\n-phiX174\t1200\t1210\t481153.85\n-phiX174\t1210\t1220\t561346.15\n-phiX174\t1220\t1230\t481153.85\n-phiX174\t1230\t1240\t449076.92\n-phiX174\t1240\t1250\t352846.15\n-phiX174\t1250\t1260\t336807.69\n-phiX174\t1260\t1270\t400961.54\n-phiX174\t1270\t1280\t352846.15\n-phiX174\t1280\t1290\t368884.62\n-phiX174\t1290\t1300\t320769.23\n-phiX174\t1300\t1310\t384923.08\n-phiX174\t1310\t1320\t513230.77\n-phiX174\t1320\t1330\t497192.31\n-phiX174\t1330\t1340\t513230.77\n-phiX174\t1340\t1350\t481153.85\n-phiX174\t1350\t1370\t497192.31\n-phiX174\t1370\t1390\t465115.38\n-phiX174\t1390\t1400\t352846.15\n-phiX174\t1400\t1410\t449076.92\n-phiX174\t1410\t1430\t481153.85\n-phiX174\t1430\t1450\t545307.69\n-phiX174\t1450\t1460\t561346.15\n-phiX174\t1460\t1470\t577384.62\n-phiX174\t1470\t1480\t609461.54\n-phiX174\t1480\t1490\t593423.08\n-phiX174\t1490\t1500\t545307.69\n-phiX174\t1500\t1510\t657576.92\n-phiX174\t1510\t1520\t625500.00\n-phiX174\t1520\t1540\t785884.62\n-phiX174\t1540\t1550\t721730.77\n-phiX174\t1550\t1570\t753807.69\n-phiX174\t1570\t1580\t769846.15\n-phiX174\t1580\t1590\t673615.38\n-phiX174\t1590\t1600\t625500.00\n-phiX174\t1600\t1610\t561346.15\n-phiX174\t1610\t1620\t529269.23\n-phiX174\t1620\t1630\t497192.31\n-phiX174\t1630\t1640\t465115.38\n-phiX174\t1640\t1650\t481153.85\n-phiX174\t1650\t1'..b'+phiX174\t3800\t3810\t423873.63\n+phiX174\t3810\t3820\t456479.29\n+phiX174\t3820\t3830\t440176.46\n+phiX174\t3830\t3840\t554296.28\n+phiX174\t3840\t3850\t635810.44\n+phiX174\t3850\t3860\t782535.93\n+phiX174\t3860\t3870\t815141.59\n+phiX174\t3870\t3880\t782535.93\n+phiX174\t3880\t3890\t733627.43\n+phiX174\t3890\t3900\t684718.93\n+phiX174\t3900\t3910\t652113.27\n+phiX174\t3910\t3920\t603204.78\n+phiX174\t3920\t3930\t4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diff -r 17d456f4051b -r aee77c22123d test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 14:38:45 2016 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt Tue Sep 20 03:07:09 2016 -0400
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@@ -1,6 +1,8 @@
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+BAM file : 0.bam
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-
 Fragment lengths:
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diff -r 17d456f4051b -r aee77c22123d test-data/plotEnrichment_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 17d456f4051b -r aee77c22123d test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular Fri May 13 14:38:45 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular Tue Sep 20 03:07:09 2016 -0400
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@@ -1,239 +1,239 @@
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b
diff -r 17d456f4051b -r aee77c22123d tool_dependencies.xml
--- a/tool_dependencies.xml Fri May 13 14:38:45 2016 -0400
+++ b/tool_dependencies.xml Tue Sep 20 03:07:09 2016 -0400
b
@@ -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>
-    <package name="deepTools" version="2.2.3">
-        <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>