Mercurial > repos > bgruening > deeptools_plot_correlation
changeset 2:c5634baf9bf9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4e5124484b42d4ffef76af4bd82a6feb67a5b829
| author | bgruening |
|---|---|
| date | Fri, 18 Dec 2015 12:27:26 -0500 |
| parents | 08b01bdab227 |
| children | e556e34fc12a |
| files | deepTools_macros.xml plotCorrelation.xml static/images/bamFP_galaxy_output.png |
| diffstat | 3 files changed, 34 insertions(+), 33 deletions(-) [+] |
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--- a/deepTools_macros.xml Fri Dec 18 08:00:49 2015 -0500 +++ b/deepTools_macros.xml Fri Dec 18 12:27:26 2015 -0500 @@ -42,24 +42,11 @@ #if $zMax: --zMax $zMax #end if - --colorMap '$colorMap' + --colorMap '$colorMap' $plotNumbers + --plotTitle $plotTitle </token> - <expand macro="plotTitle" /> - <expand macro="plotNumbers" /> - <conditional name="output"> - <param name="showOutputSettings" type="select" label="Show advanced output settings" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="no" /> - <when value="yes"> - <expand macro="input_image_file_format"/> - <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> - <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/> - </when> - </conditional> <xml name="includeZeros"> <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" @@ -102,7 +89,7 @@ <xml name="kmeans_clustering"> <conditional name="used_multiple_regions"> - <param name="used_multiple_regions_options" type="select" + <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> <option value="yes">Yes, I used multiple groups of regions</option> @@ -115,7 +102,7 @@ <option value="kmeans">Kmeans clustering</option> </param> <when value="kmeans"> - <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" + <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> </when> <when value="none" /> @@ -154,7 +141,7 @@ <xml name="plotNumbers"> <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" - label="Plot the correlation value" + label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap."/> </xml> @@ -274,9 +261,9 @@ 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://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ +.. _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://github.com/fidelram/deepTools/wiki/ +.. _help site: https://deeptools.readthedocs.org/ </token> <xml name="citations"> @@ -294,7 +281,7 @@ <xml name="multiple_input_bigwigs"> <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" - label="Bigwig file" + label="Bigwig file" help="The Bigwig file must be sorted."/> </xml> @@ -360,8 +347,8 @@ <xml name="effectiveGenomeSize"> <conditional name="effectiveGenomeSize"> <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" - help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. - Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. + help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> <option value="93260000">ce10 (93260000)</option> <option value="121400000">dm3 (121400000)</option> @@ -445,7 +432,7 @@ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> <filter> (( - output['showOutputSettings'] == 'yes' and + output['showOutputSettings'] == 'yes' and output['saveMatrix'] is True )) </filter> @@ -456,7 +443,7 @@ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> <filter> (( - output['showOutputSettings'] == 'yes' and + output['showOutputSettings'] == 'yes' and output['saveData'] is True )) </filter> @@ -464,7 +451,7 @@ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> <filter> (( - output['showOutputSettings'] == 'yes' and + output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] is True )) </filter>
--- a/plotCorrelation.xml Fri Dec 18 08:00:49 2015 -0500 +++ b/plotCorrelation.xml Fri Dec 18 12:27:26 2015 -0500 @@ -1,5 +1,5 @@ <tool id="deeptools_plot_correlation" name="plotCorrelation" version="@WRAPPER_VERSION@.0"> - <description>creates a heatmap for a score associated to genomic regions</description> + <description>creates a heatmap of correlation scores between different samples </description> <macros> <token name="@BINARY@">plotCorrelation</token> <import>deepTools_macros.xml</import> @@ -25,8 +25,8 @@ <expand macro="corMethod" /> <param argument="--whatToPlot" type="select" label="Plotting type"> - <option value="heatmap" selected="True">Spearman</option> - <option value="scatterplot">Pearson</option> + <option value="heatmap" selected="True">Heatmap</option> + <option value="scatterplot">Scatterplot</option> </param> <expand macro="skipZeros" /> @@ -77,10 +77,24 @@ <![CDATA[ **What it does** -Tool for visualizing a correlation using either bamCorrelate or -bigwigCorrelate. Pearson or Spearman methods are available to compute correlation -coefficients. Results can be saved into a heat map image or as multiple -scatter plots. Further output files are optional. +This tools takes a compressed matrix of scores (such as read coverages) for a number of genomic regions +and different samples. It can visualize the correlation among samples as scatterplots or as +heatmap of correlation coefficients. Further output files are optional. +The compressed input matrices are easily generated using the "bamCorrelate" and "bigwigCorrelate" modules of deeptools. + + +.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png + :alt: Heatmap of RNA Polymerase II ChIP-seq + + +You can find more details on plotCorrelation here http://deeptools.readthedocs.org/en/release-1.6/content/tools/plotCorrelation.html + + +**Output files**: + +- **correlation structure**: a scatterplot of all mutual correlations between all samples in matrix +- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example +- data matrix (optional): if you want to analyze or plot the correlation values using a different program, e.g. R, this matrix can be used -----