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Changeset 0:9987ddd67710 (2023-05-19)

Next changeset 1:f6f246438eda (2023-06-01)

Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5

diff -r 000000000000 -r 9987ddd67710 bigwigAverage.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigAverage.xml Fri May 19 08:30:42 2023 +0000

[

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+<tool id="deeptools_bigwig_average" name="bigwigAverage" version="@WRAPPER_VERSION@+galaxy0">
+    <description>normalizes and average multiple bigWig files</description>
+    <macros>
+        <token name="@BINARY@">bigwigAverage</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command>
+<![CDATA[
+        @BINARY@
+            @THREADS@
+            --bigwigs
+            #for $b in $bigwigs:
+                $b
+            #end for
+            --outFileName '$outFileName'
+            --outFileFormat '$outFileFormat'
+
+            #if str($region).strip() != '':
+                --region '$region'
+            #end if
+
+            #if $advancedOpt.showAdvancedOpt == "yes":
+
+              $advancedOpt.skipNAs
+              --scaleFactors '$advancedOpt.scaleFactors'
+              --binSize $advancedOpt.binSize
+
+                @blacklist@
+
+            #end if
+]]>
+    </command>
+    <inputs>
+        <param name="bigwigs" format="bigwig" type="data" label="Treatment bigwig file" multiple="true" />
+
+        <param name="outFileFormat" type="select" label="Coverage file format">
+            <option value="bigwig" selected="true">bigwig</option>
+            <option value="bedgraph">bedgraph</option>
+        </param>
+
+        <expand macro="region_limit_operation" />
+
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param argument="--binSize" type="integer" value="50" min="1"
+                    label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
+                    help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
+
+                <expand macro="skipNAs" />
+                <param name="scaleFactors" type="text" value="1" label="Scale factors (one per bigwig separated by ':')" />
+                <expand macro="blacklist" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="outFileName">
+            <change_format>
+                <when input="outFileFormat" value="bigwig" format="bigwig" />
+                <when input="outFileFormat" value="bedgraph" format="bedgraph" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bigwigs" value="test.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="binSize" value="5" />
+            <output name="outFileName" file="test_compated.bw" ftype="bigwig"
+            compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="bigwigs" value="test.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="binSize" value="5" />
+            <param name="scaleFactors" value="0.5"/>
+            <output name="outFileName" file="test_half.bw" ftype="bigwig"
+                    compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="binSize" value="5" />
+            <param name="scaleFactors" value="0.5"/>
+            <output name="outFileName" file="bigwigAverage2.bw" ftype="bigwig"
+            compare="sim_size" delta="500" />
+        </test>
+        <test>
+            <param name="bigwigs" value="test.bw,test_half.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="binSize" value="5" />
+            <param name="scaleFactors" value="1:2"/>
+            <output name="outFileName" file="test_compated.bw" ftype="bigwig"
+            compare="sim_size" delta="500" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+What it does
+--------------
+
+This tool compute average of multiple bigWig files based on the number of mapped reads. To
+average the bigwig files, the genome is partitioned into bins of equal size,
+then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, an average value is reported.
+
+Note that you can actually produce a human-readable bedGraph format instead of the compressed bigWig format if you're interested in having a look at the values yourself.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>

diff -r 000000000000 -r 9987ddd67710 deepTools_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml Fri May 19 08:30:42 2023 +0000

b'@@ -0,0 +1,942 @@\n+<macros>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+ <token name="@WRAPPER_VERSION@">3.5.1.0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="3.5.1">deeptools</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ </requirements>\n+ <expand macro="stdio" />\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\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="@PLOTWIDTHHEIGHT@">\n+ --plotWidth \'$advancedOpt.plotWidth\'\n+ --plotHeight \'$advancedOpt.plotHeight\'\n+ </token>\n+\n+ <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">\n+ <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"\n+ label="Plot height"\n+ help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />\n+\n+ <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"\n+ label="Plot width"\n+ help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />\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+ #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 $advancedOpt.transcript_id_designator\n+ #end if\n+ </token>\n+\n+ <xml name="heatmap_options">\n+ <expand macro="zMin_zMax" />\n+ <expand macro="colorMap" />\n+ <expand macro="plotTitle" />\n+ <expand macro="plotNumbers" />\n+ </xml>\n+\n+ <token name="@HEATMAP_OPTIONS@">\n+ #if str($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/CRAM files are included. The default behavior is to ignore such regions." '..b'ption 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+ <option value="Wistia_r">Wistia reversed</option>\n+ <option value="cividis_r">cividis reversed</option>\n+ <option value="icefire_r">icefire reversed</option>\n+ <option value="inferno_r">inferno reversed</option>\n+ <option value="magma_r">magma reversed</option>\n+ <option value="mako_r">mako reversed</option>\n+ <option value="nipy_spectral_r">nipy_spectral reversed</option>\n+ <option value="plasma_r">plasma reversed</option>\n+ <option value="rocket_r">rocket reversed</option>\n+ <option value="tab10_r">tab10 reversed</option>\n+ <option value="tab20_r">tab20 reversed</option>\n+ <option value="tab20b_r">tab20b reversed</option>\n+ <option value="tab20c_r">tab20c reversed</option>\n+ <option value="twilight_r">twilight reversed</option>\n+ <option value="twilight_shifted_r">twilight_shifted reversed</option>\n+ <option value="viridis_r">viridis reversed</option>\n+ <option value="vlag_r">vlag reversed</option>\n+ </param>\n+\n+ </xml>\n+\n+</macros>\n'

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diff -r 000000000000 -r 9987ddd67710 test-data/alignmentSieve.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.bed Fri May 19 08:30:42 2023 +0000

b'@@ -0,0 +1,4261 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t9813\t9912\n+chr2L\t9816\t10018\n+chr2L\t9813\t9950\n+chr2L\t9820\t9978\n+chr2L\t9823\t9949\n+chr2L\t9823\t9975\n+chr2L\t9827\t9949\n+chr2L\t9827\t9955\n+chr2L\t9828\t9936\n+chr2L\t9832\t9954\n+chr2L\t9832\t9971\n+chr2L\t9833\t9942\n+chr2L\t9833\t9953\n+chr2L\t9830\t9942\n+chr2L\t9833\t9973\n+chr2L\t9830\t9950\n+chr2L\t9833\t9942\n+chr2L\t9833\t9932\n+chr2L\t9830\t10006\n+chr2L\t9830\t9974\n+chr2L\t9830\t9946\n+chr2L\t9833\t9971\n+chr2L\t9833\t9932\n+chr2L\t9834\t9960\n+chr2L\t9844\t9953\n+chr2L\t9849\t9973\n+chr2L\t9850\t9974\n+chr2L\t9853\t9972\n+chr2L\t9850\t9955\n+chr2L\t9853\t9997\n+chr2L\t9850\t9972\n+chr2L\t9853\t10029\n+chr2L\t9854\t10017\n+chr2L\t9851\t10003\n+chr2L\t9851\t9938\n+chr2L\t9853\t9959\n+chr2L\t9854\t10005\n+chr2L\t9854\t9973\n+chr2L\t9862\t10010\n+chr2L\t9861\t10031\n+chr2L\t9866\t10039\n+chr2L\t9868\t10017\n+chr2L\t9869\t10018\n+chr2L\t9867\t10011\n+chr2L\t9867\t10022\n+chr2L\t9867\t10025\n+chr2L\t9871\t10024\n+chr2L\t9871\t10075\n+chr2L\t9871\t10004\n+chr2L\t9868\t10025\n+chr2L\t9868\t9959\n+chr2L\t9868\t9957\n+chr2L\t9871\t9975\n+chr2L\t9875\t9961\n+chr2L\t9872\t10030\n+chr2L\t9875\t10009\n+chr2L\t9875\t9961\n+chr2L\t9876\t10017\n+chr2L\t9876\t10024\n+chr2L\t9883\t10018\n+chr2L\t9880\t10025\n+chr2L\t9883\t10004\n+chr2L\t9884\t10046\n+chr2L\t9884\t10030\n+chr2L\t9884\t10144\n+chr2L\t9884\t10018\n+chr2L\t9886\t10017\n+chr2L\t9891\t10018\n+chr2L\t9894\t9972\n+chr2L\t9896\t10054\n+chr2L\t9896\t10050\n+chr2L\t9898\t10077\n+chr2L\t9900\t10050\n+chr2L\t9903\t10055\n+chr2L\t9903\t10049\n+chr2L\t9903\t10056\n+chr2L\t9900\t10064\n+chr2L\t9903\t10067\n+chr2L\t9903\t10067\n+chr2L\t9900\t10076\n+chr2L\t9903\t10062\n+chr2L\t9904\t10018\n+chr2L\t9901\t10030\n+chr2L\t9904\t10063\n+chr2L\t9904\t10073\n+chr2L\t9901\t10019\n+chr2L\t9901\t10018\n+chr2L\t9904\t10046\n+chr2L\t9904\t10055\n+chr2L\t9904\t10072\n+chr2L\t9901\t10051\n+chr2L\t9904\t10029\n+chr2L\t9904\t10017\n+chr2L\t9904\t10068\n+chr2L\t9904\t10050\n+chr2L\t9904\t10072\n+chr2L\t9904\t10049\n+chr2L\t9904\t10067\n+chr2L\t9904\t10049\n+chr2L\t9901\t10047\n+chr2L\t9905\t10050\n+chr2L\t9907\t10049\n+chr2L\t9904\t10047\n+chr2L\t9904\t10030\n+chr2L\t9907\t10067\n+chr2L\t9907\t10036\n+chr2L\t9904\t10026\n+chr2L\t9914\t10068\n+chr2L\t9914\t10017\n+chr2L\t9916\t10048\n+chr2L\t9919\t10068\n+chr2L\t9916\t10064\n+chr2L\t9918\t10019\n+chr2L\t9919\t10068\n+chr2L\t9924\t10069\n+chr2L\t9921\t10056\n+chr2L\t9927\t10019\n+chr2L\t9931\t10067\n+chr2L\t9929\t10090\n+chr2L\t9932\t10072\n+chr2L\t9931\t10089\n+chr2L\t9935\t10100\n+chr2L\t9935\t10072\n+chr2L\t9935\t10067\n+chr2L\t9933\t10089\n+chr2L\t9935\t10088\n+chr2L\t9936\t10045\n+chr2L\t9939\t10094\n+chr2L\t9937\t10030\n+chr2L\t9942\t10135\n+chr2L\t9957\t10049\n+chr2L\t9958\t10095\n+chr2L\t9958\t10106\n+chr2L\t9961\t10088\n+chr2L\t9958\t10086\n+chr2L\t9962\t10089\n+chr2L\t9962\t10100\n+chr2L\t9964\t10108\n+chr2L\t9967\t10088\n+chr2L\t9964\t10073\n+chr2L\t9968\t10134\n+chr2L\t9965\t10068\n+chr2L\t9968\t10107\n+chr2L\t9968\t10067\n+chr2L\t9966\t10089\n+chr2L\t9966\t10074\n+chr2L\t9969\t10089\n+chr2L\t9971\t10089\n+chr2L\t9969\t10103\n+chr2L\t9969\t10142\n+chr2L\t9969\t10094\n+chr2L\t9970\t10106\n+chr2L\t9973\t10132\n+chr2L\t9973\t10121\n+chr2L\t9973\t10116\n+chr2L\t9973\t10095\n+chr2L\t9971\t10280\n+chr2L\t9974\t10113\n+chr2L\t9971\t10088\n+chr2L\t9974\t10116\n+chr2L\t9974\t10088\n+chr2L\t9974\t10117\n+chr2L\t9974\t10134\n+chr2L\t9974\t10104\n+chr2L\t9972\t10141\n+chr2L\t9972\t10073\n+chr2L\t9977\t10101\n+chr2L\t9980\t10118\n+chr2L\t9981\t10125\n+chr2L\t9985\t10135\n+chr2L\t9985\t10134\n+chr2L\t9982\t10133\n+chr2L\t9982\t10237\n+chr2L\t9985\t10113\n+chr2L\t9985\t10134\n+chr2L\t9986\t10362\n+chr2L\t9983\t10146\n+chr2L\t9986\t10132\n+chr2L\t9983\t10141\n+chr2L\t9986\t10149\n+chr2L\t9986\t10141\n+chr2L\t9983\t10142\n+chr2L\t9986\t10100\n+chr2L\t9986\t10134\n+chr2L\t9983\t10136\n+chr2L\t9983\t10108\n+chr2L\t9986\t10141\n+chr2L\t9987\t10121\n+chr2L\t9987\t10134\n+chr2L\t9984\t10141\n+chr2L\t9987\t10089\n+chr2L\t9989\t10171\n+chr2L\t9989\t10099\n+chr2L\t9989\t10141\n+chr2L\t9992\t10134\n+chr2L\t9989\t10158\n+chr2L\t9992\t10150\n+chr2L\t9993\t10147\n+chr2L\t9990\t10108\n+chr2L\t9990\t10142\n+chr2L\t9993\t10170\n+chr2L\t9990\t10135\n+chr2L\t9993\t10091\n+chr2L\t9994\t10135\n+chr2L\t9991\t10145\n+chr2L\t9991\t10101\n+chr2L\t9991\t10145\n+chr2L\t9991\t10133\n+chr2L\t9999\t10134\n+chr2L\t10000\t10173\n'

diff -r 000000000000 -r 9987ddd67710 test-data/alignmentSieve.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignmentSieve.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,3 @@
+#bamFilterReads --filterMetrics
+#File Reads Remaining Total Initial Reads
+paired_chr2L.bam 8440 12644

diff -r 000000000000 -r 9987ddd67710 test-data/alignmentSieve2.bam

Binary file test-data/alignmentSieve2.bam has changed

diff -r 000000000000 -r 9987ddd67710 test-data/alignmentSieve3.bam

Binary file test-data/alignmentSieve3.bam has changed

diff -r 000000000000 -r 9987ddd67710 test-data/bamCompare_result1.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCompare_result1.bg Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,1 @@
+chrM 0 16569 1

diff -r 000000000000 -r 9987ddd67710 test-data/bamCompare_result2.bw

Binary file test-data/bamCompare_result2.bw has changed

diff -r 000000000000 -r 9987ddd67710 test-data/bamCoverage_result1.bw

Binary file test-data/bamCoverage_result1.bw has changed

diff -r 000000000000 -r 9987ddd67710 test-data/bamCoverage_result2.bw

Binary file test-data/bamCoverage_result2.bw has changed

diff -r 000000000000 -r 9987ddd67710 test-data/bamCoverage_result3.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result3.bg Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,7 @@
+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

diff -r 000000000000 -r 9987ddd67710 test-data/bamCoverage_result4.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamCoverage_result4.bg Fri May 19 08:30:42 2023 +0000

b'@@ -0,0 +1,472 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diff -r 000000000000 -r 9987ddd67710 test-data/bamPEFragmentSize_histogram_result1.png

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diff -r 000000000000 -r 9987ddd67710 test-data/bamPEFragmentSize_lengths1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_lengths1.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,5 @@
+#bamPEFragmentSize
+Size Occurrences Sample
+241 1 bowtie2 test1.bam
+242 1 bowtie2 test1.bam
+251 1 bowtie2 test1.bam

diff -r 000000000000 -r 9987ddd67710 test-data/bamPEFragmentSize_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_result1.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,46 @@
+
+
+Sample label: bowtie2 test1.bam
+Sample size: 3
+
+Fragment lengths:
+Min.: 241.0
+1st Qu.: 241.5
+Mean: 244.66666666666666
+Median: 242.0
+3rd Qu.: 246.5
+Max.: 251.0
+Std: 4.496912521077347
+MAD: 1.0
+Len. 10%: 241.2
+Len. 20%: 241.4
+Len. 30%: 241.6
+Len. 40%: 241.8
+Len. 60%: 243.8
+Len. 70%: 245.6
+Len. 80%: 247.4
+Len. 90%: 249.2
+Len. 99%: 250.82
+
+
+Read lengths:
+Sample size: 3
+
+Min.: 251.0
+1st Qu.: 251.0
+Mean: 251.0
+Median: 251.0
+3rd Qu.: 251.0
+Max.: 251.0
+Std: 0.0
+MAD: 0.0
+Len. 10%: 251.0
+Len. 20%: 251.0
+Len. 30%: 251.0
+Len. 40%: 251.0
+Len. 60%: 251.0
+Len. 70%: 251.0
+Len. 80%: 251.0
+Len. 90%: 251.0
+Len. 99%: 251.0
+

diff -r 000000000000 -r 9987ddd67710 test-data/bamPEFragmentSize_table1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,2 @@
+ Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99%
+bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.2 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0

diff -r 000000000000 -r 9987ddd67710 test-data/bigwigAverage2.bw

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diff -r 000000000000 -r 9987ddd67710 test-data/bigwigCompare_result2.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwigCompare_result2.bg Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,3 @@
+ch1 0 400 1
+ch2 0 400 1
+ch3 0 400 1

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diff -r 000000000000 -r 9987ddd67710 test-data/computeGCBias_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeGCBias_result1.tabular Fri May 19 08:30:42 2023 +0000

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diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrix1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix1.bed Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,8 @@
+phiX174 1000 1500 CG11023 0 +
+phiX174 150 1750 cda5 0 -
+phiX174 150 177 cda8 0 -
+phiX174 75 1500 cda9 0 +
+phiX174 101 175 C11023 0 +
+phiX174 125 150 ca5 0 -
+phiX174 450 1750 ca8 0 +
+phiX174 80 1500 cda9 0 +

diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrix2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrix2.bed Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,6 @@
+ch1 100 150 CG11023 0 +
+ch2 150 175 cda5 0 -
+ch3 100 125 cda8 0 +
+ch1 75 125 C11023 0 +
+ch2 125 150 ca5 0 -
+ch3 75 100 ca8 0 +

diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrix2.bw

Binary file test-data/computeMatrix2.bw has changed

diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrixOperations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/computeMatrixOperations.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,4 @@
+Groups:
+ genes
+Samples:
+ bamCoverage_result4_bw_0

diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrixOperations_result2.mat.gz

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diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrix_result1.gz

Binary file test-data/computeMatrix_result1.gz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrix_result2.gz

Binary file test-data/computeMatrix_result2.gz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/computeMatrix_result3.gz

Binary file test-data/computeMatrix_result3.gz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/correctGCBias_result1.bam

Binary file test-data/correctGCBias_result1.bam has changed

diff -r 000000000000 -r 9987ddd67710 test-data/estimateReadFiltering.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/estimateReadFiltering.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,3 @@
+Sample Total Reads Mapped Reads Alignments in blacklisted regions Estimated mapped reads filtered Below MAPQ Missing Flags Excluded Flags Internally-determined Duplicates Marked Duplicates Singletons Wrong strand
+paired_chr2L.bam 12644 12589 0 4192.0 4149.0 0.0 0.0 0.0 0.0 55.0 0.0
+paired_chr2L.bam 12644 12589 0 4192.0 4149.0 0.0 0.0 0.0 0.0 55.0 0.0

diff -r 000000000000 -r 9987ddd67710 test-data/heatmapper_result1.png

Binary file test-data/heatmapper_result1.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/heatmapper_result2.png

Binary file test-data/heatmapper_result2.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/heatmapper_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1 2
+file_0 genes 2477942.34473 2610259.65234

diff -r 000000000000 -r 9987ddd67710 test-data/multiBamSummary_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBamSummary_regions.bed Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,3 @@
+chrM 1 10
+chrM 5 15
+chrM 10 20

diff -r 000000000000 -r 9987ddd67710 test-data/multiBamSummary_result1.npz

Binary file test-data/multiBamSummary_result1.npz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/multiBamSummary_result2.npz

Binary file test-data/multiBamSummary_result2.npz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/multiBamSummary_result2b.npz

Binary file test-data/multiBamSummary_result2b.npz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/multiBigwigSummary_result1.npz

Binary file test-data/multiBigwigSummary_result1.npz has changed

diff -r 000000000000 -r 9987ddd67710 test-data/multiBigwigSummary_result1.png

Binary file test-data/multiBigwigSummary_result1.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/multiBigwigSummary_result2.npz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.npz Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,121 @@
+#'chr' 'start' 'end' 'sample1' 'sample2'
+ch1 0 10 0.0 0.0
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diff -r 000000000000 -r 9987ddd67710 test-data/multiBigwigSummary_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.tabular Fri May 19 08:30:42 2023 +0000

diff -r 000000000000 -r 9987ddd67710 test-data/paired_chr2L.bam

Binary file test-data/paired_chr2L.bam has changed

diff -r 000000000000 -r 9987ddd67710 test-data/paired_chr2L.cram

Binary file test-data/paired_chr2L.cram has changed

diff -r 000000000000 -r 9987ddd67710 test-data/phiX.2bit

Binary file test-data/phiX.2bit has changed

diff -r 000000000000 -r 9987ddd67710 test-data/phiX.bam

Binary file test-data/phiX.bam has changed

diff -r 000000000000 -r 9987ddd67710 test-data/phiX.bam.bai

Binary file test-data/phiX.bam.bai has changed

diff -r 000000000000 -r 9987ddd67710 test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
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+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
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+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
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+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

diff -r 000000000000 -r 9987ddd67710 test-data/plotCorrelation_result1.png

Binary file test-data/plotCorrelation_result1.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/plotCorrelation_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCorrelation_result1.tabular Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,4 @@
+#plotCorrelation --outFileCorMatrix
+ 'bowtie2 test1.bam' 'bowtie2 test1.bam'
+'bowtie2 test1.bam' 1.0000 1.0000
+'bowtie2 test1.bam' 1.0000 1.0000

diff -r 000000000000 -r 9987ddd67710 test-data/plotCorrelation_result2.png

Binary file test-data/plotCorrelation_result2.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/plotCoverage.metrics
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage.metrics Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,9 @@
+Sample Threshold Percent
+bowtie2 test1.bam 0 100.000
+bowtie2 test1.bam 0 100.000
+bowtie2 test1.bam 5 1.509
+bowtie2 test1.bam 5 1.509
+bowtie2 test1.bam 10 1.461
+bowtie2 test1.bam 10 1.461
+bowtie2 test1.bam 20 1.406
+bowtie2 test1.bam 20 1.406

diff -r 000000000000 -r 9987ddd67710 test-data/plotCoverage_result1.png

Binary file test-data/plotCoverage_result1.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/plotCoverage_result1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage_result1.tabular Fri May 19 08:30:42 2023 +0000

b"@@ -0,0 +1,16571 @@\n+#plotCoverage --outRawCounts\n+#'chr'\t'start'\t'end'\t'bowtie2 test1.bam'\t'bowtie2 test1.bam'\n+chrM\t0\t1\t23.0\t23.0\n+chrM\t1\t2\t35.0\t35.0\n+chrM\t2\t3\t35.0\t35.0\n+chrM\t3\t4\t35.0\t35.0\n+chrM\t4\t5\t35.0\t35.0\n+chrM\t5\t6\t35.0\t35.0\n+chrM\t6\t7\t35.0\t35.0\n+chrM\t7\t8\t35.0\t35.0\n+chrM\t8\t9\t35.0\t35.0\n+chrM\t9\t10\t35.0\t35.0\n+chrM\t10\t11\t35.0\t35.0\n+chrM\t11\t12\t35.0\t35.0\n+chrM\t12\t13\t35.0\t35.0\n+chrM\t13\t14\t35.0\t35.0\n+chrM\t14\t15\t35.0\t35.0\n+chrM\t15\t16\t35.0\t35.0\n+chrM\t16\t17\t35.0\t35.0\n+chrM\t17\t18\t35.0\t35.0\n+chrM\t18\t19\t35.0\t35.0\n+chrM\t19\t20\t35.0\t35.0\n+chrM\t20\t21\t35.0\t35.0\n+chrM\t21\t22\t35.0\t35.0\n+chrM\t22\t23\t35.0\t35.0\n+chrM\t23\t24\t35.0\t35.0\n+chrM\t24\t25\t35.0\t35.0\n+chrM\t25\t26\t35.0\t35.0\n+chrM\t26\t27\t35.0\t35.0\n+chrM\t27\t28\t35.0\t35.0\n+chrM\t28\t29\t35.0\t35.0\n+chrM\t29\t30\t35.0\t35.0\n+chrM\t30\t31\t35.0\t35.0\n+chrM\t31\t32\t35.0\t35.0\n+chrM\t32\t33\t35.0\t35.0\n+chrM\t33\t34\t35.0\t35.0\n+chrM\t34\t35\t35.0\t35.0\n+chrM\t35\t36\t35.0\t35.0\n+chrM\t36\t37\t35.0\t35.0\n+chrM\t37\t38\t35.0\t35.0\n+chrM\t38\t39\t35.0\t35.0\n+chrM\t39\t40\t35.0\t35.0\n+chrM\t40\t41\t35.0\t35.0\n+chrM\t41\t42\t35.0\t35.0\n+chrM\t42\t43\t35.0\t35.0\n+chrM\t43\t44\t35.0\t35.0\n+chrM\t44\t45\t35.0\t35.0\n+chrM\t45\t46\t35.0\t35.0\n+chrM\t46\t47\t35.0\t35.0\n+chrM\t47\t48\t35.0\t35.0\n+chrM\t48\t49\t35.0\t35.0\n+chrM\t49\t50\t35.0\t35.0\n+chrM\t50\t51\t35.0\t35.0\n+chrM\t51\t52\t35.0\t35.0\n+chrM\t52\t53\t35.0\t35.0\n+chrM\t53\t54\t35.0\t35.0\n+chrM\t54\t55\t35.0\t35.0\n+chrM\t55\t56\t35.0\t35.0\n+chrM\t56\t57\t35.0\t35.0\n+chrM\t57\t58\t35.0\t35.0\n+chrM\t58\t59\t35.0\t35.0\n+chrM\t59\t60\t35.0\t35.0\n+chrM\t60\t61\t35.0\t35.0\n+chrM\t61\t62\t35.0\t35.0\n+chrM\t62\t63\t35.0\t35.0\n+chrM\t63\t64\t35.0\t35.0\n+chrM\t64\t65\t35.0\t35.0\n+chrM\t65\t66\t35.0\t35.0\n+chrM\t66\t67\t35.0\t35.0\n+chrM\t67\t68\t35.0\t35.0\n+chrM\t68\t69\t35.0\t35.0\n+chrM\t69\t70\t35.0\t35.0\n+chrM\t70\t71\t35.0\t35.0\n+chrM\t71\t72\t35.0\t35.0\n+chrM\t72\t73\t35.0\t35.0\n+chrM\t73\t74\t35.0\t35.0\n+chrM\t74\t75\t35.0\t35.0\n+chrM\t75\t76\t35.0\t35.0\n+chrM\t76\t77\t35.0\t35.0\n+chrM\t77\t78\t35.0\t35.0\n+chrM\t78\t79\t35.0\t35.0\n+chrM\t79\t80\t35.0\t35.0\n+chrM\t80\t81\t35.0\t35.0\n+chrM\t81\t82\t35.0\t35.0\n+chrM\t82\t83\t35.0\t35.0\n+chrM\t83\t84\t35.0\t35.0\n+chrM\t84\t85\t35.0\t35.0\n+chrM\t85\t86\t35.0\t35.0\n+chrM\t86\t87\t35.0\t35.0\n+chrM\t87\t88\t35.0\t35.0\n+chrM\t88\t89\t35.0\t35.0\n+chrM\t89\t90\t35.0\t35.0\n+chrM\t90\t91\t35.0\t35.0\n+chrM\t91\t92\t35.0\t35.0\n+chrM\t92\t93\t35.0\t35.0\n+chrM\t93\t94\t35.0\t35.0\n+chrM\t94\t95\t35.0\t35.0\n+chrM\t95\t96\t35.0\t35.0\n+chrM\t96\t97\t35.0\t35.0\n+chrM\t97\t98\t35.0\t35.0\n+chrM\t98\t99\t35.0\t35.0\n+chrM\t99\t100\t35.0\t35.0\n+chrM\t100\t101\t35.0\t35.0\n+chrM\t101\t102\t35.0\t35.0\n+chrM\t102\t103\t35.0\t35.0\n+chrM\t103\t104\t35.0\t35.0\n+chrM\t104\t105\t35.0\t35.0\n+chrM\t105\t106\t35.0\t35.0\n+chrM\t106\t107\t35.0\t35.0\n+chrM\t107\t108\t35.0\t35.0\n+chrM\t108\t109\t35.0\t35.0\n+chrM\t109\t110\t35.0\t35.0\n+chrM\t110\t111\t35.0\t35.0\n+chrM\t111\t112\t35.0\t35.0\n+chrM\t112\t113\t35.0\t35.0\n+chrM\t113\t114\t35.0\t35.0\n+chrM\t114\t115\t35.0\t35.0\n+chrM\t115\t116\t35.0\t35.0\n+chrM\t116\t117\t35.0\t35.0\n+chrM\t117\t118\t35.0\t35.0\n+chrM\t118\t119\t35.0\t35.0\n+chrM\t119\t120\t35.0\t35.0\n+chrM\t120\t121\t35.0\t35.0\n+chrM\t121\t122\t35.0\t35.0\n+chrM\t122\t123\t35.0\t35.0\n+chrM\t123\t124\t35.0\t35.0\n+chrM\t124\t125\t35.0\t35.0\n+chrM\t125\t126\t35.0\t35.0\n+chrM\t126\t127\t35.0\t35.0\n+chrM\t127\t128\t35.0\t35.0\n+chrM\t128\t129\t35.0\t35.0\n+chrM\t129\t130\t35.0\t35.0\n+chrM\t130\t131\t35.0\t35.0\n+chrM\t131\t132\t35.0\t35.0\n+chrM\t132\t133\t35.0\t35.0\n+chrM\t133\t134\t35.0\t35.0\n+chrM\t134\t135\t35.0\t35.0\n+chrM\t135\t136\t35.0\t35.0\n+chrM\t136\t137\t35.0\t35.0\n+chrM\t137\t138\t35.0\t35.0\n+chrM\t138\t139\t35.0\t35.0\n+chrM\t139\t140\t35.0\t35.0\n+chrM\t140\t141\t35.0\t35.0\n+chrM\t141\t142\t35.0\t35.0\n+chrM\t142\t143\t35.0\t35.0\n+chrM\t143\t144\t35.0\t35.0\n+chrM\t144\t145\t35.0\t35.0\n+chrM\t145\t146\t35.0\t35.0\n+chrM\t146\t147\t35.0\t35.0\n+chrM\t147\t148\t35.0\t35.0\n+chrM\t148\t149\t35.0\t35.0\n+chrM\t149\t150\t35.0\t35.0\n+chrM\t150\t151\t35.0\t35.0\n+chrM\t151\t152\t35.0\t35.0\n+chrM\t152\t153\t35.0\t35.0\n+chrM\t153\t154\t35.0\t35.0\n+chrM\t154\t155\t35.0\t35.0\n+chrM\t155\t156\t35.0\t35.0\n+chrM\t156\t157\t35.0\t35.0\n+chrM\t157\t158\t35.0\t35.0\n+chrM\t158\t159\t35.0\t35.0\n+chrM\t159\t160\t35.0\t35.0\n+chrM\t160\t161\t35.0\t35.0\n+chrM\t161\t162\t35.0\t35.0\n+chrM\t162\t163\t35.0\t35.0\n+chrM\t163\t164\t35.0\t35.0\n+chrM\t164\t165\t35.0\t35.0\n+chrM\t165\t166\t35.0\t35.0\n+chrM\t166\t167\t35.0\t35.0\n+chrM\t167\t168\t35.0\t35.0\n+chrM\t168\t169\t35.0\t35.0\n+chrM\t169\t170\t35.0\t35.0\n+chrM\t170\t171\t35.0\t35.0\n+"..b'\t16415\t16416\t0.0\t0.0\n+chrM\t16416\t16417\t0.0\t0.0\n+chrM\t16417\t16418\t0.0\t0.0\n+chrM\t16418\t16419\t0.0\t0.0\n+chrM\t16419\t16420\t0.0\t0.0\n+chrM\t16420\t16421\t0.0\t0.0\n+chrM\t16421\t16422\t0.0\t0.0\n+chrM\t16422\t16423\t0.0\t0.0\n+chrM\t16423\t16424\t0.0\t0.0\n+chrM\t16424\t16425\t0.0\t0.0\n+chrM\t16425\t16426\t0.0\t0.0\n+chrM\t16426\t16427\t0.0\t0.0\n+chrM\t16427\t16428\t0.0\t0.0\n+chrM\t16428\t16429\t0.0\t0.0\n+chrM\t16429\t16430\t0.0\t0.0\n+chrM\t16430\t16431\t0.0\t0.0\n+chrM\t16431\t16432\t0.0\t0.0\n+chrM\t16432\t16433\t0.0\t0.0\n+chrM\t16433\t16434\t0.0\t0.0\n+chrM\t16434\t16435\t0.0\t0.0\n+chrM\t16435\t16436\t0.0\t0.0\n+chrM\t16436\t16437\t0.0\t0.0\n+chrM\t16437\t16438\t0.0\t0.0\n+chrM\t16438\t16439\t0.0\t0.0\n+chrM\t16439\t16440\t0.0\t0.0\n+chrM\t16440\t16441\t0.0\t0.0\n+chrM\t16441\t16442\t0.0\t0.0\n+chrM\t16442\t16443\t0.0\t0.0\n+chrM\t16443\t16444\t0.0\t0.0\n+chrM\t16444\t16445\t0.0\t0.0\n+chrM\t16445\t16446\t0.0\t0.0\n+chrM\t16446\t16447\t0.0\t0.0\n+chrM\t16447\t16448\t0.0\t0.0\n+chrM\t16448\t16449\t0.0\t0.0\n+chrM\t16449\t16450\t0.0\t0.0\n+chrM\t16450\t16451\t0.0\t0.0\n+chrM\t16451\t16452\t0.0\t0.0\n+chrM\t16452\t16453\t0.0\t0.0\n+chrM\t16453\t16454\t0.0\t0.0\n+chrM\t16454\t16455\t0.0\t0.0\n+chrM\t16455\t16456\t0.0\t0.0\n+chrM\t16456\t16457\t0.0\t0.0\n+chrM\t16457\t16458\t0.0\t0.0\n+chrM\t16458\t16459\t0.0\t0.0\n+chrM\t16459\t16460\t0.0\t0.0\n+chrM\t16460\t16461\t0.0\t0.0\n+chrM\t16461\t16462\t0.0\t0.0\n+chrM\t16462\t16463\t0.0\t0.0\n+chrM\t16463\t16464\t0.0\t0.0\n+chrM\t16464\t16465\t0.0\t0.0\n+chrM\t16465\t16466\t0.0\t0.0\n+chrM\t16466\t16467\t0.0\t0.0\n+chrM\t16467\t16468\t0.0\t0.0\n+chrM\t16468\t16469\t0.0\t0.0\n+chrM\t16469\t16470\t0.0\t0.0\n+chrM\t16470\t16471\t0.0\t0.0\n+chrM\t16471\t16472\t0.0\t0.0\n+chrM\t16472\t16473\t0.0\t0.0\n+chrM\t16473\t16474\t0.0\t0.0\n+chrM\t16474\t16475\t0.0\t0.0\n+chrM\t16475\t16476\t0.0\t0.0\n+chrM\t16476\t16477\t0.0\t0.0\n+chrM\t16477\t16478\t0.0\t0.0\n+chrM\t16478\t16479\t0.0\t0.0\n+chrM\t16479\t16480\t0.0\t0.0\n+chrM\t16480\t16481\t0.0\t0.0\n+chrM\t16481\t16482\t0.0\t0.0\n+chrM\t16482\t16483\t0.0\t0.0\n+chrM\t16483\t16484\t0.0\t0.0\n+chrM\t16484\t16485\t0.0\t0.0\n+chrM\t16485\t16486\t0.0\t0.0\n+chrM\t16486\t16487\t0.0\t0.0\n+chrM\t16487\t16488\t0.0\t0.0\n+chrM\t16488\t16489\t0.0\t0.0\n+chrM\t16489\t16490\t0.0\t0.0\n+chrM\t16490\t16491\t0.0\t0.0\n+chrM\t16491\t16492\t0.0\t0.0\n+chrM\t16492\t16493\t0.0\t0.0\n+chrM\t16493\t16494\t0.0\t0.0\n+chrM\t16494\t16495\t0.0\t0.0\n+chrM\t16495\t16496\t0.0\t0.0\n+chrM\t16496\t16497\t0.0\t0.0\n+chrM\t16497\t16498\t0.0\t0.0\n+chrM\t16498\t16499\t0.0\t0.0\n+chrM\t16499\t16500\t0.0\t0.0\n+chrM\t16500\t16501\t0.0\t0.0\n+chrM\t16501\t16502\t0.0\t0.0\n+chrM\t16502\t16503\t0.0\t0.0\n+chrM\t16503\t16504\t0.0\t0.0\n+chrM\t16504\t16505\t0.0\t0.0\n+chrM\t16505\t16506\t0.0\t0.0\n+chrM\t16506\t16507\t0.0\t0.0\n+chrM\t16507\t16508\t0.0\t0.0\n+chrM\t16508\t16509\t0.0\t0.0\n+chrM\t16509\t16510\t0.0\t0.0\n+chrM\t16510\t16511\t0.0\t0.0\n+chrM\t16511\t16512\t0.0\t0.0\n+chrM\t16512\t16513\t0.0\t0.0\n+chrM\t16513\t16514\t0.0\t0.0\n+chrM\t16514\t16515\t0.0\t0.0\n+chrM\t16515\t16516\t0.0\t0.0\n+chrM\t16516\t16517\t0.0\t0.0\n+chrM\t16517\t16518\t0.0\t0.0\n+chrM\t16518\t16519\t0.0\t0.0\n+chrM\t16519\t16520\t0.0\t0.0\n+chrM\t16520\t16521\t0.0\t0.0\n+chrM\t16521\t16522\t0.0\t0.0\n+chrM\t16522\t16523\t0.0\t0.0\n+chrM\t16523\t16524\t0.0\t0.0\n+chrM\t16524\t16525\t0.0\t0.0\n+chrM\t16525\t16526\t0.0\t0.0\n+chrM\t16526\t16527\t0.0\t0.0\n+chrM\t16527\t16528\t0.0\t0.0\n+chrM\t16528\t16529\t0.0\t0.0\n+chrM\t16529\t16530\t0.0\t0.0\n+chrM\t16530\t16531\t0.0\t0.0\n+chrM\t16531\t16532\t0.0\t0.0\n+chrM\t16532\t16533\t0.0\t0.0\n+chrM\t16533\t16534\t0.0\t0.0\n+chrM\t16534\t16535\t0.0\t0.0\n+chrM\t16535\t16536\t0.0\t0.0\n+chrM\t16536\t16537\t0.0\t0.0\n+chrM\t16537\t16538\t0.0\t0.0\n+chrM\t16538\t16539\t0.0\t0.0\n+chrM\t16539\t16540\t0.0\t0.0\n+chrM\t16540\t16541\t0.0\t0.0\n+chrM\t16541\t16542\t0.0\t0.0\n+chrM\t16542\t16543\t0.0\t0.0\n+chrM\t16543\t16544\t0.0\t0.0\n+chrM\t16544\t16545\t0.0\t0.0\n+chrM\t16545\t16546\t0.0\t0.0\n+chrM\t16546\t16547\t0.0\t0.0\n+chrM\t16547\t16548\t0.0\t0.0\n+chrM\t16548\t16549\t0.0\t0.0\n+chrM\t16549\t16550\t0.0\t0.0\n+chrM\t16550\t16551\t0.0\t0.0\n+chrM\t16551\t16552\t0.0\t0.0\n+chrM\t16552\t16553\t0.0\t0.0\n+chrM\t16553\t16554\t0.0\t0.0\n+chrM\t16554\t16555\t0.0\t0.0\n+chrM\t16555\t16556\t0.0\t0.0\n+chrM\t16556\t16557\t0.0\t0.0\n+chrM\t16557\t16558\t0.0\t0.0\n+chrM\t16558\t16559\t0.0\t0.0\n+chrM\t16559\t16560\t0.0\t0.0\n+chrM\t16560\t16561\t0.0\t0.0\n+chrM\t16561\t16562\t0.0\t0.0\n+chrM\t16562\t16563\t0.0\t0.0\n+chrM\t16563\t16564\t0.0\t0.0\n+chrM\t16564\t16565\t0.0\t0.0\n+chrM\t16565\t16566\t0.0\t0.0\n+chrM\t16566\t16567\t0.0\t0.0\n+chrM\t16567\t16568\t0.0\t0.0\n+chrM\t16568\t16569\t0.0\t0.0\n'

diff -r 000000000000 -r 9987ddd67710 test-data/plotEnrichment_output.png

Binary file test-data/plotEnrichment_output.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/plotEnrichment_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotEnrichment_output.txt Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,5 @@
+file featureType percent featureReadCount totalReadCount
+bowtie2 test1.bam up 100.00 47 47
+bowtie2 test1.bam down 100.00 47 47
+bowtie2 test1.bam up 100.00 47 47
+bowtie2 test1.bam down 100.00 47 47

diff -r 000000000000 -r 9987ddd67710 test-data/plotFingerprint_quality_metrics.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotFingerprint_quality_metrics.tabular Fri May 19 08:30:42 2023 +0000

@@ -0,0 +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 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 nan 0.2690044980681214 nan nan nan
+bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.2690044980681214 0 0 0

diff -r 000000000000 -r 9987ddd67710 test-data/plotFingerprint_result1.png

Binary file test-data/plotFingerprint_result1.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/plotFingerprint_result2.png

Binary file test-data/plotFingerprint_result2.png has changed

diff -r 000000000000 -r 9987ddd67710 test-data/plotFingerprint_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotFingerprint_result2.tabular Fri May 19 08:30:42 2023 +0000

b"@@ -0,0 +1,16072 @@\n+#plotFingerprint --outRawCounts\n+'bowtie2 test1.bam'\t'bowtie2 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diff -r 000000000000 -r 9987ddd67710 test-data/plotPCA_result1.png

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diff -r 000000000000 -r 9987ddd67710 test-data/plotPCA_result2.png

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diff -r 000000000000 -r 9987ddd67710 test-data/plotPCA_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,4 @@
+#plotPCA --outFileNameData
+Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue
+1 -0.7071067811865476 -0.7071067811865475 4.0
+2 -0.7071067811865475 0.7071067811865476 2.49319462166397e-32

diff -r 000000000000 -r 9987ddd67710 test-data/profiler_result1.png

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diff -r 000000000000 -r 9987ddd67710 test-data/profiler_result2.png

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diff -r 000000000000 -r 9987ddd67710 test-data/profiler_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1.0 2.0
+bamCoverage_result4_bw_0 genes 2477942.875 2610260.125

diff -r 000000000000 -r 9987ddd67710 test-data/sequence.2bit

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diff -r 000000000000 -r 9987ddd67710 test-data/test.bw

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diff -r 000000000000 -r 9987ddd67710 test-data/test_compated.bw

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diff -r 000000000000 -r 9987ddd67710 test-data/test_half.bw

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diff -r 000000000000 -r 9987ddd67710 tool-data/deepTools_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/deepTools_seqs.loc.sample Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,27 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with deepTools. You will
+#need to supply these files and then create a deepTools_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The deepTools_seqs.loc
+#file has this format:
+#
+#<unique_build_id> <display_name> <file_path>
+#
+#So, for example, if your deepTools_seqs.loc began like this:
+#
+#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
+#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
+#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your deepTools_seqs.loc file should include an entry per line for
+#each file you have stored that you want to be available. Note that
+#your files should all have the extension '2bit'.
+#
+#Please note that the <unique_build_id> is also used as "Species name abbreviation".

diff -r 000000000000 -r 9987ddd67710 tool-data/lastz_seqs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with deepTools.
+#This file is named lastz_seqs.loc file to make use of an already existing loc
+#file from the lastz tool that is created by the twobit data-manager.
+#You will need to supply these files and then create a lastz_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The lastz_seqs.loc
+#file has this format:
+#
+#<unique_build_id> <display_name> <file_path>
+#
+#So, for example, if your lastz_seqs.loc began like this:
+#
+#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
+#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
+#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your lastz_seqs.loc file should include an entry per line for
+#each file you have stored that you want to be available. Note that
+#your files should all have the extension '2bit'.
+#
+#Please note that the <unique_build_id> is also used as "Species name abbreviation".

diff -r 000000000000 -r 9987ddd67710 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri May 19 08:30:42 2023 +0000

@@ -0,0 +1,8 @@
+
+<tables>
+    
+    <table name="lastz_seqs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/lastz_seqs.loc" />
+    </table>
+</tables>