# HG changeset patch # User bgruening # Date 1455550440 18000 # Node ID 275ed3e83de0d9818127159c02e43fa96af40e1e # Parent 14cb57237e46d57cd71102b387a249c509c2665f planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920 diff -r 14cb57237e46 -r 275ed3e83de0 computeMatrix.xml --- a/computeMatrix.xml Mon Jan 25 20:26:32 2016 -0500 +++ b/computeMatrix.xml Mon Feb 15 10:34:00 2016 -0500 @@ -8,18 +8,25 @@ @@ -164,19 +170,21 @@ + label="Convert missing values to 0?" + help="If set to 'yes', missing values (NAs) are converted + to 0. If you want to use clustering with plotHeatmap + or plotProfile, set this to 'yes'. + The default is to ignore missing values, which will be + depicted as black areas once a heatmap is created. + (--missingDataAsZero)" /> - - @@ -233,27 +240,80 @@ `_. + +The intermediate file produced by ``computeMatrix`` is meant to be used with ``plotHeatmap`` and ``plotProfile``. +See the descriptions of ``plotHeatmap`` and ``plotProfile`` for example plots. + +.. image:: $PATH_TO_IMAGES/computeMatrix_overview.png + :alt: Relationship between computeMatrix, heatmapper and profiler + :width: 600 + :height: 418 + +======= + +Usage hints +------------- -Genomic regions can really be anything - genes, parts of genes, ChIP-seq -peaks, favorite genome regions... as long as you provide a proper file -in BED or INTERVAL format. If you would like to compare different groups of regions -(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group. +The supplied genomic regions can really be anything - genes, parts of genes, ChIP-seq peaks, favorite genome regions... as long as you provide a proper file +in BED or INTERVAL format. If you would like to compare different groups of regions (e.g., genes from chromosome 2 and 3), you can supply more than 1 regions file, one for each group by selecting "Insert Select regions". + +.. image:: $PATH_TO_IMAGES/computeMatrix_selectRegions.png + :width: 600 + :height: 150 + +You can select as many score (bigWig) files as you like. Simply use the Shift and/or Command key while clicking on the files of interest. -computeMatrix can also be used to filter and sort -regions according to their score by making use of its advanced output options. +.. image:: $PATH_TO_IMAGES/computeMatrix_selectScores.png + :width: 600 + :height: 136 + +The multitude of parameters can seem daunting at first - here are the options that we tend to tune most often: + +* ``bin Size`` -- The default value works well most of the time, but if you want to have a more finely grained image, decrease the default value (but not smaller than your bigWig file(s)' bin size). If you want to reduce the computation time, increase it. +* ``Skip zeros`` -- useful to avoid completely blank lines in the heatmap. +* ``Convert missing values to 0?`` -- If you want to identify clusters of similar regions in an unsupervised fashion using ``plotHeatmap`` and/or ``plotProfile``, you should definitely set this to 'yes'. -.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png - :alt: Relationship between computeMatrix, heatmapper and profiler +Output files +--------------- + +The default output is a **gzipped table of values** that is used by both ``plotHeatmap`` and ``plotProfile``. + +The optional output files include a) the **regions after sorting and filtering (if selected)** as they were used to calculate the values for the plotting, and b) the uncompressed table that **underlies the heatmap**. + +**TIP:** ``computeMatrix`` can also be used to filter and sort regions according to their score by making use of the "advanced output settings". + +.. image:: $PATH_TO_IMAGES/computeMatrix_advancedOutput.png + :width: 600 + :height: 189 +.. image:: $PATH_TO_IMAGES/computeMatrix_output.png + :width: 600 + :height: 297 -You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeMatrix.html +Note that these advanced output options are available for ``plotHeatmap`` and ``plotProfile``, too. + +See the following table for the optional output options: ++-----------------------------------+--------------------+-----------------+-----------------+ +| **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** | ++-----------------------------------+--------------------+-----------------+-----------------+ +| values underlying the heatmap | yes | yes | no | ++-----------------------------------+--------------------+-----------------+-----------------+ +| values underlying the profile | no | no | yes | ++-----------------------------------+--------------------+-----------------+-----------------+ +| sorted and/or filtered regions | yes | yes | yes | ++-----------------------------------+--------------------+-----------------+-----------------+ + +**More examples** can be found in our `Gallery `_. ----- diff -r 14cb57237e46 -r 275ed3e83de0 deepTools_macros.xml --- a/deepTools_macros.xml Mon Jan 25 20:26:32 2016 -0500 +++ b/deepTools_macros.xml Mon Feb 15 10:34:00 2016 -0500 @@ -72,12 +72,12 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 2.0.1 + 2.1.0 python @BINARY@ - deepTools + deepTools @@ -104,6 +104,7 @@ + + + + @@ -126,6 +136,11 @@ --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans #end if #end if + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': + #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: + --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust + #end if + #end if #end if @@ -293,6 +308,12 @@ + + + + @@ -310,6 +331,7 @@ help="Title of the plot, to be printed on top of the generated image." /> + + + + + + + + + + + + + + + + + #if $advancedOpt.doExtendCustom.doExtend == 'custom': + --extendReads $advancedOpt.doExtendCustom.extendReadsValue + #else if $advancedOpt.doExtendCustom.doExtend == 'yes': + --extendReads + #end if + $advancedOpt.ignoreDuplicates + $advancedOpt.centerReads + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + #if $advancedOpt.samFlagInclude: + --samFlagInclude $advancedOpt.samFlagInclude + #end if + #if $advancedOpt.samFlagExclude: + --samFlagExclude $advancedOpt.samFlagExclude + #end if + + + + + + + + + + + #if str($plotting_type.zMin) != "": + --zMin $plotting_type.zMin + #end if + #if str($plotting_type.zMax) != "": + --zMax $plotting_type.zMax + #end if + --colorMap '$plotting_type.colorMap' + $plotting_type.plotNumbers + --plotTitle '$plotting_type.plotTitle' + + + + + + + + + + + + + + + + + --numberOfProcessors "\${GALAXY_SLOTS:-4}" +<<<<<<< HEAD + 2.0.1.0 +======= + 2.1.0 +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + + + python + @BINARY@ +<<<<<<< HEAD + deepTools +======= + deepTools +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + + + + @BINARY@ --version + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': + #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: + --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust + #end if + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + +.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac +.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de +.. _help site: https://deeptools.readthedocs.org/ + + + + + 10.1093/nar/gku365 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "$source.input1_2bit.fields.path" + #end if + + + + + + + + + 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d56067f86089e75354a2fad266002db3730766d9 + + + + + + + + + + + + + + + + + + + + + + + + + + + https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz + + + + $INSTALL_DIR/bin + $INSTALL_DIR + $INSTALL_DIR + $INSTALL_DIR + $INSTALL_DIR/bin + + $ENV[LIBPNG_LIB_PATH] + $ENV[LIBPNG_LIB_PATH] + + TRUE + + + + + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + + +