Mercurial > repos > bgruening > deeptools_bigwig_correlate
changeset 7:e9e05e3b69fd draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41
| author | bgruening |
|---|---|
| date | Wed, 23 Dec 2015 03:52:30 -0500 |
| parents | 841ade9fb784 |
| children | d7961ecf5290 |
| files | bigwigCorrelate.xml deepTools_macros.xml static/images/plotCorrelation_galaxy_bw_heatmap_output.png test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/plotPCA_result1.png test-data/profiler_result2.png tool_dependencies.xml |
| diffstat | 9 files changed, 27 insertions(+), 21 deletions(-) [+] |
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--- a/bigwigCorrelate.xml Tue Dec 22 13:39:43 2015 -0500 +++ b/bigwigCorrelate.xml Wed Dec 23 03:52:30 2015 -0500 @@ -1,9 +1,9 @@ <tool id="deeptools_bigwig_correlate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0"> - <description>calculates average read coverages for a list of two or more bigwig files</description> + <description>correlates pairs of BigWig files</description> <macros> <token name="@BINARY@">bigwigCorrelate</token> <import>deepTools_macros.xml</import> - </macros> + </macros> <expand macro="requirements" /> <command> <![CDATA[ @@ -22,7 +22,7 @@ --labels '#echo "' '".join($labels)#' #if $outRawCounts: - --outRawCounts '$outFileRawCounts' + --outRawCounts '$outFileRawCounts' #end if #if $mode.modeOpt == "bins": @@ -42,7 +42,7 @@ <expand macro="multiple_input_bigwigs" /> <conditional name="mode"> - <param name="modeOpt" type="select" label="Choose computation mode" + <param name="modeOpt" type="select" label="Choose computation mode" help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in @@ -51,7 +51,7 @@ <option value="BED-file">Limit correlation to certain regions (BED file)</option> </param> <when value="bins"> - <param name="binSize" type="integer" value="10000" min="1" + <param name="binSize" type="integer" value="10000" min="1" label="Bin size in bp" help="Length in base pairs for a window used to sample the genome. (--binSize)"/> @@ -96,18 +96,19 @@ <![CDATA[ **What it does** -Given two or more bigWig files, bigwigCorrelate computes the average scores for each of the files in every genomic region. -This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions -in 'BED-file' mode. Most commonly, the output of bigwigCorrelate is used by other tools such as 'plotCorrelation' or 'plotPCA' -for visualization and diagnostic purposes. +bigwigCorrelate computes the overall similarity between two or more bigWig +files based on coverage means of genomic regions. The correlation analysis +is performed for the entire genome by running the program in 'bins' mode, +or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses +are available to compute correlation coefficients. Results are saved to a +heat map file. Further output files are optional. **Output files**: -- **Coverage scores**: Coverage scores computed and saved in a format detected by 'plotCorrelation' or 'plotPCA' tools. +- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation +- data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used -- Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values - or compute statistics yourself using a different program (like R). -----
--- a/deepTools_macros.xml Tue Dec 22 13:39:43 2015 -0500 +++ b/deepTools_macros.xml Wed Dec 23 03:52:30 2015 -0500 @@ -40,10 +40,10 @@ </xml> <token name="@HEATMAP_OPTIONS@"> - #if str($plotting_type.zMin) != "": + #if $plotting_type.zMin: --zMin $plotting_type.zMin #end if - #if str($plotting_type.zMax) != "": + #if $plotting_type.zMax: --zMax $plotting_type.zMax #end if --colorMap '$plotting_type.colorMap' @@ -107,11 +107,7 @@ </param> <when value="kmeans"> <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: 0 [do not cluster])."/> + 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" /> </conditional> @@ -412,6 +408,7 @@ <when value="no" /> <when value="yes"> <yield /> + <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> </when> </conditional> @@ -459,6 +456,14 @@ </xml> <xml name="output_graphic_outputs"> + <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveData'] is True + )) + </filter> + </data> <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> <filter> ((
--- a/test-data/bamCoverage_result3.bg Tue Dec 22 13:39:43 2015 -0500 +++ b/test-data/bamCoverage_result3.bg Wed Dec 23 03:52:30 2015 -0500 @@ -5,4 +5,4 @@ chrM 220 230 7690304.31 chrM 230 240 6027535.81 chrM 240 250 3325537.00 -chrM 250 16569 623538.2 +chrM 250 260 623538.19
--- a/tool_dependencies.xml Tue Dec 22 13:39:43 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 23 03:52:30 2015 -0500 @@ -4,6 +4,6 @@ <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deepTools" version="2.0"> - <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>