Previous changeset 16:9ccbe8e8fd74 (2018-02-05) Next changeset 18:396dfbc32304 (2018-03-02) |
Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty |
modified:
deepTools_macros.xml plotPCA.xml readme.rst test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_result1.txt test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/plotCorrelation_result1.tabular test-data/plotCorrelation_result2.png test-data/plotCoverage_result1.png test-data/plotCoverage_result1.tabular test-data/plotEnrichment_output.txt test-data/plotFingerprint_result2.tabular test-data/plotPCA_result1.png test-data/plotPCA_result2.tabular |
added:
test-data/alignmentSieve.bam test-data/alignmentSieve.bed test-data/alignmentSieve.txt test-data/alignmentSieve2.bam test-data/alignmentSieve3.bam test-data/bamPEFragmentSize_lengths1.txt test-data/bamPEFragmentSize_table1.txt test-data/estimateReadFiltering.txt test-data/paired_chr2L.cram |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f deepTools_macros.xml --- a/deepTools_macros.xml Mon Feb 05 11:42:35 2018 -0500 +++ b/deepTools_macros.xml Thu Feb 15 07:39:05 2018 -0500 |
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b'@@ -1,11 +1,11 @@\n <macros>\n \n <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n- <token name="@WRAPPER_VERSION@">2.5.7</token>\n+ <token name="@WRAPPER_VERSION@">3.0.0</token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="2.5.7">deeptools</requirement>\n- <yield />\n+ <requirement type="package" version="3.0.0">deeptools</requirement>\n+ <requirement type="package" version="1.7">samtools</requirement>\n </requirements>\n <expand macro="stdio" />\n <version_command>@BINARY@ --version</version_command>\n@@ -100,7 +100,7 @@\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+ help="If set, then regions with zero counts for *all* BAM/CRAM files are included. The default behavior is to ignore such regions." />\n </xml>\n \n <xml name="zMin_zMax">\n@@ -238,7 +238,7 @@\n <xml name="extendReads">\n <conditional name="doExtendCustom">\n <param name="doExtend" type="select" label="Extend reads to the given average fragment size."\n- help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.\n+ help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.\n By default *each* read mate is extended.\n This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.\n Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.\n@@ -312,7 +312,7 @@\n <xml name="sortRegions">\n <param argument="--sortRegions" type="select" label="Sort regions"\n help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">\n- <option value="no">no ordering</option>\n+ <option value="no">maintain the same ordering as the input files</option>\n <option value="descend" selected="true">descending order</option>\n <option value="ascend">ascending order</option>\n </param>\n@@ -321,19 +321,19 @@\n <xml name="minMappingQuality">\n <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"\n label="Minimum mapping quality"\n- help= "If set, only reads with a mapping quality score higher than this value are considered."/>\n+ help= "If set, only reads with a mapping quality score at least this high are considered."/>\n </xml>\n \n <xml name="skipZeros">\n <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""\n label ="Skip zeros"\n- help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />\n+ help ="If set, then zero counts that happen for *all* BAM/CRAM files given are ignored. This may result in fewer considered regions." />\n </xml>\n \n <xml name="fragmentLength">\n- <param argument="--fragmentLength" type="integer" value="300" min="1"\n+ <param argument="--fragmentLength" type="integer" min="1" optional="true"\n label="Fragment length used for the sequencing"\n- help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>\n+ help ="If paired-end reads are'..b'ed="true">hg19 (2451960000)</option>\n- <option value="2150570000">mm9 (2150570000)</option>\n+ <option value="130428560">dm3 (130428560)</option>\n+ <option value="125464728">dm6 (125464728)</option>\n+ <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>\n+ <option value="2701495761">GRCh38/hg38 (2701495761)</option>\n+ <option value="2304947926">GRCm37/mm9 (2304947926)</option>\n+ <option value="2308125349">GRCm38/mm10 (2308125349)</option>\n <option value="specific">user specified</option>\n </param>\n <when value="specific">\n <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"\n- help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n+ help="e.g. ce10: 93260000, dm3: 130428560, hg19: 2685511504, mm9: 2304947926"/>\n </when>\n- <when value="2150570000" />\n- <when value="2451960000" />\n- <when value="121400000" />\n <when value="93260000" />\n+ <when value="130428560" />\n+ <when value="125464728" />\n+ <when value="2685511504" />\n+ <when value="2701495761" />\n+ <when value="2304947926" />\n+ <when value="2308125349" />\n </conditional>\n </xml>\n \n@@ -596,6 +617,7 @@\n <when value="yes">\n <yield />\n <param name="saveSortedRegions" type="boolean"\n+ argument="--outFileSortedRegions"\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@@ -605,11 +627,12 @@\n \n \n <xml name="input_image_file_format">\n- <param argument="--outFileFormat" type="select" label="Image file format">\n+ <param argument="--outFileFormat" type="select" label="Image file format" help="Note that the plotly output can be very large and not all options are supported.">\n <option value="png" selected="true">png</option>\n <option value="pdf">pdf</option>\n <option value="svg">svg</option>\n <option value="eps">eps</option>\n+ <option value="plotly">plotly</option>\n </param>\n </xml>\n \n@@ -624,6 +647,7 @@\n <when input="output.outFileFormat" value="pdf" format="pdf" />\n <when input="output.outFileFormat" value="svg" format="svg" />\n <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="plotly" format="html" />\n </change_format>\n </data>\n </xml>\n@@ -634,6 +658,7 @@\n <when input="outFileFormat" value="pdf" format="pdf" />\n <when input="outFileFormat" value="svg" format="svg" />\n <when input="outFileFormat" value="eps" format="eps" />\n+ <when input="outFileFormat" value="plotly" format="html" />\n </change_format>\n </data>\n </xml>\n@@ -662,8 +687,7 @@\n \n <xml name="colorMap">\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+ help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">\n <option value="RdYlBu" selected="true">RdYlBu</option>\n <option value="Accent">Accent</option>\n <option value="Spectral">Spectral</option>\n' |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f plotPCA.xml --- a/plotPCA.xml Mon Feb 05 11:42:35 2018 -0500 +++ b/plotPCA.xml Thu Feb 15 07:39:05 2018 -0500 |
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@@ -14,8 +14,15 @@ --plotFileFormat "$outFileFormat" #if str($advancedOpt.showAdvancedOpt) == 'yes': @PLOTWIDTHHEIGHT@ + $advancedOpt.log2 + --PCs $advancedOpt.PCs + --ntop $advancedOpt.ntop + $advancedOpt.transpose + $advancedOpt.rowCenter + #if $advancedOpt.colors: + --colors $advancedOpt.colors + #end if #end if - $rowCenter #if $outFileNameData --outFileNameData "$output_outFileNameData" #end if @@ -26,7 +33,6 @@ <expand macro="input_image_file_format" /> <expand macro="plotTitle" /> <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/> - <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically." truevalue="--rowCenter" falsevalue="" /> <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > <option value="no" selected="true">no</option> @@ -35,6 +41,15 @@ <when value="no" /> <when value="yes"> <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" /> + <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text" + help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." /> + <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer" + help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." /> + <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." /> + <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" /> + <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" /> + <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True" + help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." /> </when> </conditional> </inputs> @@ -49,14 +64,15 @@ <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" /> <param name="plotTitle" value="Test Plot" /> <param name="outFileFormat" value="png" /> - <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="4000" /> + <param name="showAdvancedOpt" value="yes" /> + <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" /> </test> <test> <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" /> <param name="plotTitle" value="Test Plot" /> <param name="outFileFormat" value="png" /> <param name="outFileNameData" value="True" /> - <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="4000" /> + <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" /> <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" /> </test> </tests> @@ -73,8 +89,8 @@ The result is a panel of two plots: -1. The eigenvalues of the **top two principal components**. -2. The **Scree plot** for the top five principal components where the bars represent the amount of variability explained by the individual factors and the red line traces the amount of variability is explained by the individual components in a cumulative manner +1. Either the loadings (default) or the projections (``--transpose``) of the samples on the desired **two principal components**. +2. The **Scree plot** for principal components where the bars represent the eigenvalues the red line traces the amount of variability is explained by the individual components in a cumulative manner. Example plot ------------ |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f readme.rst --- a/readme.rst Mon Feb 05 11:42:35 2018 -0500 +++ b/readme.rst Thu Feb 15 07:39:05 2018 -0500 |
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@@ -20,7 +20,7 @@ deeptools is developed under here: - https://github.com/fidelram/deepTools + https://github.com/deeptools/deepTools For support, questions, or feature requests contact: deeptools@googlegroups.com @@ -41,7 +41,7 @@ Citation ======== -deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. +deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools. ======= |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/alignmentSieve.bam |
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Binary file test-data/alignmentSieve.bam has changed |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/alignmentSieve.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignmentSieve.bed Thu Feb 15 07:39:05 2018 -0500 |
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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' |
b |
diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/alignmentSieve.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignmentSieve.txt Thu Feb 15 07:39:05 2018 -0500 |
b |
@@ -0,0 +1,3 @@ +#bamFilterReads --filterMetrics +#File Reads Remaining Total Initial Reads +paired_chr2L.bam 8440 12644 |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/alignmentSieve2.bam |
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Binary file test-data/alignmentSieve2.bam has changed |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/alignmentSieve3.bam |
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Binary file test-data/alignmentSieve3.bam has changed |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/bamPEFragmentSize_histogram_result1.png |
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Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/bamPEFragmentSize_lengths1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_lengths1.txt Thu Feb 15 07:39:05 2018 -0500 |
b |
@@ -0,0 +1,5 @@ +#bamPEFragmentSize +Size Occurrences Sample +241 1 bowtie2 test1.bam +242 1 bowtie2 test1.bam +251 1 bowtie2 test1.bam |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:42:35 2018 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Thu Feb 15 07:39:05 2018 -0500 |
b |
@@ -11,8 +11,21 @@ 3rd Qu.: 246.5 Max.: 251.0 Std: 4.496912521077347 +MAD: 1.0 +Len. 10%: 241.20000000000002 +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 @@ -20,3 +33,14 @@ 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 + |
b |
diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/bamPEFragmentSize_table1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_table1.txt Thu Feb 15 07:39:05 2018 -0500 |
b |
@@ -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 1.0 241.20000000000002 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 |
b |
diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/estimateReadFiltering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/estimateReadFiltering.txt Thu Feb 15 07:39:05 2018 -0500 |
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@@ -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 1395.9 4149.0 0.0 0.0 0.0 0.0 55.0 0.0 +paired_chr2L.bam 12644 12589 0 1395.9 4149.0 0.0 0.0 0.0 0.0 55.0 0.0 |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/heatmapper_result1.png |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/heatmapper_result2.png |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/multiBamSummary_result1.npz |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/plotCorrelation_result1.tabular --- a/test-data/plotCorrelation_result1.tabular Mon Feb 05 11:42:35 2018 -0500 +++ b/test-data/plotCorrelation_result1.tabular Thu Feb 15 07:39:05 2018 -0500 |
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@@ -1,3 +1,4 @@ +#plotCorrelation --outFileCorMatrix 'bowtie2 test1.bam' 'bowtie2 test1.bam' 'bowtie2 test1.bam' 1.0000 1.0000 'bowtie2 test1.bam' 1.0000 1.0000 |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/plotCoverage_result1.png |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/plotCoverage_result1.tabular --- a/test-data/plotCoverage_result1.tabular Mon Feb 05 11:42:35 2018 -0500 +++ b/test-data/plotCoverage_result1.tabular Thu Feb 15 07:39:05 2018 -0500 |
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@@ -1,3 +1,4 @@ +#plotCoverage --outRawCounts #'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam' chrM 0 1 23.0 23.0 chrM 1 2 35.0 35.0 |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/plotEnrichment_output.txt --- a/test-data/plotEnrichment_output.txt Mon Feb 05 11:42:35 2018 -0500 +++ b/test-data/plotEnrichment_output.txt Thu Feb 15 07:39:05 2018 -0500 |
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@@ -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 +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 |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Mon Feb 05 11:42:35 2018 -0500 +++ b/test-data/plotFingerprint_result2.tabular Thu Feb 15 07:39:05 2018 -0500 |
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@@ -1,3 +1,4 @@ +#plotFingerprint --outRawCounts 'bowtie2 test1.bam' 'bowtie2 test1.bam' 1085 1085 1782 1782 |
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diff -r 9ccbe8e8fd74 -r f2f1ca0f032f test-data/plotPCA_result2.tabular --- a/test-data/plotPCA_result2.tabular Mon Feb 05 11:42:35 2018 -0500 +++ b/test-data/plotPCA_result2.tabular Thu Feb 15 07:39:05 2018 -0500 |
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@@ -1,3 +1,4 @@ +#plotPCA --outFileNameData Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue -1 -0.7071067811865476 -0.7071067811865475 6.000000000000001 +1 -0.7071067811865476 -0.7071067811865475 4.0 2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32 |