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

Changeset 16:e6a06ce6ac46 (2018-02-05)
Previous changeset 15:29fcfd36e90a (2017-05-15) Next changeset 17:1795fdfc23b8 (2018-02-15)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c
modified:
deepTools_macros.xml
test-data/bamCoverage_result4.bg
test-data/bamCoverage_result5.bw
test-data/bamPEFragmentSize_result1.txt
test-data/heatmapper_result1.png
test-data/plotCorrelation_result1.png
test-data/plotCorrelation_result2.png
test-data/plotCoverage_result1.png
test-data/plotEnrichment_output.txt
test-data/plotFingerprint_quality_metrics.tabular
test-data/plotPCA_result1.png
test-data/plotPCA_result2.png
test-data/plotPCA_result2.tabular
test-data/profiler_result1.png
test-data/profiler_result2.png
test-data/profiler_result2.tabular
removed:
deepTools_macros.xml.orig
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diff -r 29fcfd36e90a -r e6a06ce6ac46 deepTools_macros.xml
--- a/deepTools_macros.xml Mon May 15 03:56:46 2017 -0400
+++ b/deepTools_macros.xml Mon Feb 05 11:44:01 2018 -0500
b
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.5.1.1</token>
+    <token name="@WRAPPER_VERSION@">2.5.7</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.1">deeptools</requirement>
+            <requirement type="package" version="2.5.7">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -211,7 +211,7 @@
     </xml>
 
     <xml name="gtf_options">
-        <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
+        <param argument="--metagene" type="boolean" truevalue="--metagene" 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"
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diff -r 29fcfd36e90a -r e6a06ce6ac46 deepTools_macros.xml.orig
--- a/deepTools_macros.xml.orig Mon May 15 03:56:46 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,639 +0,0 @@\n-<macros>\n-\n-    <xml name="advancedOpt_scaffold">\n-        <conditional name="advancedOpt">\n-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >\n-                <option value="no" selected="true">no</option>\n-                <option value="yes">yes</option>\n-            </param>\n-            <when value="no" />\n-            <when value="yes">\n-                <yield/>\n-            </when>\n-        </conditional>\n-    </xml>\n-\n-    <token name="@ADVANCED_OPTS_READ_PROCESSING@">\n-        #if $advancedOpt.doExtendCustom.doExtend == \'custom\':\n-            --extendReads $advancedOpt.doExtendCustom.extendReadsValue\n-        #else if $advancedOpt.doExtendCustom.doExtend == \'yes\':\n-            --extendReads\n-        #end if\n-        $advancedOpt.ignoreDuplicates\n-        $advancedOpt.centerReads\n-        #if $advancedOpt.minMappingQuality:\n-            --minMappingQuality \'$advancedOpt.minMappingQuality\'\n-        #end if\n-        #if $advancedOpt.samFlagInclude:\n-            --samFlagInclude $advancedOpt.samFlagInclude\n-        #end if\n-        #if $advancedOpt.samFlagExclude:\n-            --samFlagExclude $advancedOpt.samFlagExclude\n-        #end if\n-    </token>\n-\n-    <xml name="heatmap_options">\n-        <expand macro="zMin_zMax" />\n-        <expand macro="colorMap" />\n-        <expand macro="plotTitle" />\n-        <expand macro="plotNumbers" />\n-    </xml>\n-\n-    <token name="@HEATMAP_OPTIONS@">\n-        #if str($plotting_type.zMin) != "":\n-            --zMin $plotting_type.zMin\n-        #end if\n-        #if str($plotting_type.zMax) != "":\n-            --zMax $plotting_type.zMax\n-        #end if\n-        --colorMap \'$plotting_type.colorMap\'\n-        $plotting_type.plotNumbers\n-        --plotTitle \'$plotting_type.plotTitle\'\n-    </token>\n-\n-\n-    <xml name="includeZeros">\n-        <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""\n-            label="Include zeros"\n-            help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />\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-            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-            help="If not specified the value is set automatically."/>\n-    </xml>\n-\n-    <xml name="region_limit_operation">\n-        <param argument="--region" type="text" value=""\n-            label="Region of the genome to limit the operation to"\n-            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />\n-    </xml>\n-\n-    <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n-<<<<<<< HEAD\n-    <token name="@WRAPPER_VERSION@">2.0.1.0</token>\n-=======\n-    <token name="@WRAPPER_VERSION@">2.1.0</token>\n->>>>>>> d56067f86089e75354a2fad266002db3730766d9\n-    <xml name="requirements">\n-        <requirements>\n-            <requirement type="package" version="2.7.10">python</requirement>\n-            <requirement type="binary">@BINARY@</requirement>\n-<<<<<<< HEAD\n-            <requirement type="package" version="2.0.1">deepTools</requirement>\n-=======\n-            <requirement type="package" version="2.1.0">deepTools</requirement>\n->>>>>>> d56067f86089e75354a2fad266002db3730766d9\n-            <yield />\n-        </requirements>\n-        <expand macro="stdio" />\n-        <version_command>@BINARY@ --version</version_command>\n-    </xml>\n-\n-    <xml name="smoothLength">\n-        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"\n-            label="Smooth values using the following length (in bases)"\n-            help '..b'k2 reversed</option>\n-            <option value="Reds_r">Reds reversed</option>\n-            <option value="Oranges_r">Oranges reversed</option>\n-            <option value="Greens_r">Greens reversed</option>\n-            <option value="Blues_r">Blues reversed</option>\n-            <option value="Greys_r">Greys reversed</option>\n-            <option value="Purples_r">Purples reversed</option>\n-            <option value="Paired_r">Paired reversed</option>\n-            <option value="Pastel1_r">Pastel1 reversed</option>\n-            <option value="Pastel2_r">Pastel2 reversed</option>\n-            <option value="spring_r">spring reversed</option>\n-            <option value="summer_r">summer reversed</option>\n-            <option value="autumn_r">autumn reversed</option>\n-            <option value="winter_r">winter reversed</option>\n-            <option value="hot_r">hot reversed</option>\n-            <option value="coolwarm_r">coolwarm reversed</option>\n-            <option value="cool_r">cool reversed</option>\n-            <option value="seismic_r">seismic reversed</option>\n-            <option value="terrain_r">terrain reversed</option>\n-            <option value="ocean_r">ocean reversed</option>\n-            <option value="rainbow_r">rainbow reversed</option>\n-            <option value="bone_r">bone reversed</option>\n-            <option value="flag_r">flag reversed</option>\n-            <option value="prism_r">prism reversed</option>\n-            <option value="cubehelix_r">cubehelix reversed</option>\n-            <option value="binary_r">binary reversed</option>\n-            <option value="pink_r">pink reversed</option>\n-            <option value="gray_r">gray reversed</option>\n-            <option value="copper_r">copper reversed</option>\n-            <option value="BrBG_r">BrBG reversed</option>\n-            <option value="BuGn_r">BuGn reversed</option>\n-            <option value="BuPu_r">BuPu reversed</option>\n-            <option value="GnBu_r">GnBu reversed</option>\n-            <option value="OrRd_r">OrRd reversed</option>\n-            <option value="PiYG_r">PiYG reversed</option>\n-            <option value="PRGn_r">PRGn reversed</option>\n-            <option value="PuOr_r">PuOr reversed</option>\n-            <option value="PuRd_r">PuRd reversed</option>\n-            <option value="PuBu_r">PuBu reversed</option>\n-            <option value="RdBu_r">RdBu reversed</option>\n-            <option value="RdGy_r">RdGy reversed</option>\n-            <option value="RdPu_r">RdPu reversed</option>\n-            <option value="YlGn_r">YlGn reversed</option>\n-            <option value="PuBuGn_r">PuBuGn reversed</option>\n-            <option value="RdYlBu_r">RdYlBu reversed</option>\n-            <option value="RdYlGn_r">RdYlGn reversed</option>\n-            <option value="YlGnBu_r">YlGnBu reversed</option>\n-            <option value="YlOrBr_r">YlOrBr reversed</option>\n-            <option value="YlOrRd_r">YlOrRd reversed</option>\n-            <option value="gist_gray_r">gist_gray reversed</option>\n-            <option value="gist_stern_r">gist_stern reversed</option>\n-            <option value="gist_earth_r">gist_earth reversed</option>\n-            <option value="gist_yarg_r">gist_yarg reversed</option>\n-            <option value="gist_ncar_r">gist_ncar reversed</option>\n-            <option value="gist_rainbow_r">gist_rainbow reversed</option>\n-            <option value="gist_heat_r">gist_heat reversed</option>\n-            <option value="gnuplot_r">gnuplot reversed</option>\n-            <option value="gnuplot2_r">gnuplot2 reversed</option>\n-            <option value="CMRmap_r">CMRmap reversed</option>\n-            <option value="bwr_r">bwr reversed</option>\n-            <option value="hsv_r">hsv reversed</option>\n-            <option value="brg_r">brg reversed</option>\n-            <option value="jet_r">jet reversed</option>\n-            <option value="afmhot_r">afmhot reversed</option>\n-        </param>\n-\n-    </xml>\n-\n-</macros>\n'
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg Mon May 15 03:56:46 2017 -0400
+++ b/test-data/bamCoverage_result4.bg Mon Feb 05 11:44:01 2018 -0500
b
b'@@ -1,472 +1,472 @@\n-phiX174\t0\t10\t16302.8\n-phiX174\t10\t20\t48908.5\n-phiX174\t20\t70\t146725\n-phiX174\t70\t80\t195634\n-phiX174\t80\t90\t179331\n-phiX174\t90\t100\t163028\n-phiX174\t100\t120\t114120\n-phiX174\t120\t140\t146725\n-phiX174\t140\t150\t163028\n-phiX174\t150\t160\t130423\n-phiX174\t160\t170\t163028\n-phiX174\t170\t180\t179331\n-phiX174\t180\t200\t211937\n-phiX174\t200\t210\t195634\n-phiX174\t210\t220\t244542\n-phiX174\t220\t230\t277148\n-phiX174\t230\t240\t342359\n-phiX174\t240\t250\t326057\n-phiX174\t250\t260\t293451\n-phiX174\t260\t270\t342359\n-phiX174\t270\t280\t407571\n-phiX174\t280\t300\t423874\n-phiX174\t300\t310\t358662\n-phiX174\t310\t320\t326057\n-phiX174\t320\t330\t374965\n-phiX174\t330\t340\t358662\n-phiX174\t340\t350\t293451\n-phiX174\t350\t360\t260845\n-phiX174\t360\t370\t228240\n-phiX174\t370\t380\t244542\n-phiX174\t380\t390\t309754\n-phiX174\t390\t400\t260845\n-phiX174\t400\t410\t244542\n-phiX174\t410\t420\t228240\n-phiX174\t420\t450\t293451\n-phiX174\t450\t460\t309754\n-phiX174\t460\t470\t342359\n-phiX174\t470\t490\t423874\n-phiX174\t490\t510\t505388\n-phiX174\t510\t520\t472782\n-phiX174\t520\t530\t570599\n-phiX174\t530\t540\t505388\n-phiX174\t540\t550\t537993\n-phiX174\t550\t560\t554296\n-phiX174\t560\t570\t652113\n-phiX174\t570\t580\t635810\n-phiX174\t580\t590\t570599\n-phiX174\t590\t600\t619508\n-phiX174\t600\t610\t554296\n-phiX174\t610\t630\t635810\n-phiX174\t630\t640\t586902\n-phiX174\t640\t650\t521691\n-phiX174\t650\t660\t554296\n-phiX174\t660\t670\t570599\n-phiX174\t670\t680\t603205\n-phiX174\t680\t690\t668416\n-phiX174\t690\t700\t652113\n-phiX174\t700\t710\t570599\n-phiX174\t710\t730\t603205\n-phiX174\t730\t740\t521691\n-phiX174\t740\t760\t603205\n-phiX174\t760\t770\t505388\n-phiX174\t770\t780\t521691\n-phiX174\t780\t790\t537993\n-phiX174\t790\t800\t554296\n-phiX174\t800\t810\t456479\n-phiX174\t810\t820\t440176\n-phiX174\t820\t830\t374965\n-phiX174\t830\t840\t326057\n-phiX174\t840\t850\t358662\n-phiX174\t850\t860\t309754\n-phiX174\t860\t870\t342359\n-phiX174\t870\t880\t260845\n-phiX174\t880\t890\t358662\n-phiX174\t890\t900\t391268\n-phiX174\t900\t910\t472782\n-phiX174\t910\t920\t554296\n-phiX174\t920\t930\t570599\n-phiX174\t930\t940\t554296\n-phiX174\t940\t950\t586902\n-phiX174\t950\t960\t603205\n-phiX174\t960\t970\t521691\n-phiX174\t970\t980\t489085\n-phiX174\t980\t990\t440176\n-phiX174\t990\t1000\t423874\n-phiX174\t1000\t1010\t456479\n-phiX174\t1010\t1030\t586902\n-phiX174\t1030\t1040\t766233\n-phiX174\t1040\t1050\t798839\n-phiX174\t1050\t1060\t831444\n-phiX174\t1060\t1070\t880353\n-phiX174\t1070\t1080\t847747\n-phiX174\t1080\t1090\t880353\n-phiX174\t1090\t1100\t782536\n-phiX174\t1100\t1110\t749930\n-phiX174\t1110\t1120\t668416\n-phiX174\t1120\t1130\t652113\n-phiX174\t1130\t1140\t635810\n-phiX174\t1140\t1150\t684719\n-phiX174\t1150\t1160\t635810\n-phiX174\t1160\t1170\t603205\n-phiX174\t1170\t1180\t619508\n-phiX174\t1180\t1190\t586902\n-phiX174\t1190\t1200\t521691\n-phiX174\t1200\t1210\t489085\n-phiX174\t1210\t1220\t570599\n-phiX174\t1220\t1230\t489085\n-phiX174\t1230\t1240\t456479\n-phiX174\t1240\t1250\t358662\n-phiX174\t1250\t1260\t342359\n-phiX174\t1260\t1270\t407571\n-phiX174\t1270\t1280\t358662\n-phiX174\t1280\t1290\t374965\n-phiX174\t1290\t1300\t326057\n-phiX174\t1300\t1310\t391268\n-phiX174\t1310\t1320\t521691\n-phiX174\t1320\t1330\t505388\n-phiX174\t1330\t1340\t521691\n-phiX174\t1340\t1350\t489085\n-phiX174\t1350\t1370\t505388\n-phiX174\t1370\t1390\t472782\n-phiX174\t1390\t1400\t358662\n-phiX174\t1400\t1410\t456479\n-phiX174\t1410\t1430\t489085\n-phiX174\t1430\t1450\t554296\n-phiX174\t1450\t1460\t570599\n-phiX174\t1460\t1470\t586902\n-phiX174\t1470\t1480\t619508\n-phiX174\t1480\t1490\t603205\n-phiX174\t1490\t1500\t554296\n-phiX174\t1500\t1510\t668416\n-phiX174\t1510\t1520\t635810\n-phiX174\t1520\t1540\t798839\n-phiX174\t1540\t1550\t733627\n-phiX174\t1550\t1570\t766233\n-phiX174\t1570\t1580\t782536\n-phiX174\t1580\t1590\t684719\n-phiX174\t1590\t1600\t635810\n-phiX174\t1600\t1610\t570599\n-phiX174\t1610\t1620\t537993\n-phiX174\t1620\t1630\t505388\n-phiX174\t1630\t1640\t472782\n-phiX174\t1640\t1650\t489085\n-phiX174\t1650\t1660\t505388\n-phiX174\t1660\t1670\t537993\n-phiX174\t1670\t1680\t603205\n-phiX174\t1680\t1690\t521691\n-phiX174\t1690\t1700\t537993\n-phiX174\t1700\t1710\t603205\n-phiX174\t1710\t1720\t554296\n-phiX174\t1720\t1730\t537993\n-phiX174\t1730\t1740\t586902\n-phiX174\t1740\t1750\t537993\n-phiX174\t1750\t1760\t440176\n-phiX174\t1760\t1770\t423874\n-phiX174\t1770\t1780\t374965\n-phiX174\t1780\t1790\t358662\n-phiX174\t1790\t1810\t342359\n-phiX174\t1810\t1820\t326057\n-phiX174\t1820\t1830\t47278'..b'\t3620\t3630\t400962\n+phiX174\t3630\t3640\t384923\n+phiX174\t3640\t3650\t352846\n+phiX174\t3650\t3660\t433038\n+phiX174\t3660\t3680\t400962\n+phiX174\t3680\t3690\t417000\n+phiX174\t3690\t3700\t336808\n+phiX174\t3700\t3710\t384923\n+phiX174\t3710\t3720\t433038\n+phiX174\t3720\t3730\t625500\n+phiX174\t3730\t3740\t593423\n+phiX174\t3740\t3750\t705692\n+p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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/bamCoverage_result5.bw
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Mon May 15 03:56:46 2017 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:44:01 2018 -0500
b
@@ -6,11 +6,11 @@
 Fragment lengths:
 Min.: 241.0
 1st Qu.: 241.5
-Mean: 244.666666667
+Mean: 244.66666666666666
 Median: 242.0
 3rd Qu.: 246.5
 Max.: 251.0
-Std: 4.49691252108
+Std: 4.496912521077347
 
 Read lengths:
 Min.: 251.0
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/heatmapper_result1.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotCorrelation_result1.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotCoverage_result1.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotEnrichment_output.txt
--- a/test-data/plotEnrichment_output.txt Mon May 15 03:56:46 2017 -0400
+++ b/test-data/plotEnrichment_output.txt Mon Feb 05 11:44:01 2018 -0500
b
@@ -1,5 +1,5 @@
 file featureType percent
+bowtie2 test1.bam up 100.00
 bowtie2 test1.bam down 100.00
 bowtie2 test1.bam up 100.00
 bowtie2 test1.bam down 100.00
-bowtie2 test1.bam up 100.00
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular Mon May 15 03:56:46 2017 -0400
+++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Feb 05 11:44:01 2018 -0500
b
@@ -1,3 +1,3 @@
 Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence
-bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA
-bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0
+bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 NA 0.26900449806812143 NA NA NA
+bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.26900449806812143 0 0 0
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotPCA_result1.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotPCA_result2.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/plotPCA_result2.tabular
--- a/test-data/plotPCA_result2.tabular Mon May 15 03:56:46 2017 -0400
+++ b/test-data/plotPCA_result2.tabular Mon Feb 05 11:44:01 2018 -0500
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@@ -1,3 +1,3 @@
 Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue
-1 -0.707106781187 -0.707106781187 6.0
-2 -0.707106781187 0.707106781187 1.23259516441e-32
+1 -0.7071067811865476 -0.7071067811865475 6.000000000000001
+2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/profiler_result1.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/profiler_result2.png
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diff -r 29fcfd36e90a -r e6a06ce6ac46 test-data/profiler_result2.tabular
--- a/test-data/profiler_result2.tabular Mon May 15 03:56:46 2017 -0400
+++ b/test-data/profiler_result2.tabular Mon Feb 05 11:44:01 2018 -0500
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@@ -1,3 +1,3 @@
 bin labels -0.0Kb 0.0Kb
-bins 1 2
+bins 1.0 2.0
 bamCoverage_result4_bw_0 genes 2477942.875 2610260.125