Mercurial > repos > bgruening > deeptools_plot_heatmap
changeset 28:42cb23d80271 draft
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
| author | bgruening |
|---|---|
| date | Fri, 11 Feb 2022 16:10:54 +0000 |
| parents | a4dfb122e52b |
| children | ba6efa77fb79 |
| files | deepTools_macros.xml plotHeatmap.xml readme.rst repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/bamPEFragmentSize_table1.txt test-data/plotFingerprint_quality_metrics.tabular test-data/plotPCA_result2.tabular |
| diffstat | 8 files changed, 48 insertions(+), 96 deletions(-) [+] |
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--- a/deepTools_macros.xml Sat Jan 25 05:15:40 2020 -0500 +++ b/deepTools_macros.xml Fri Feb 11 16:10:54 2022 +0000 @@ -1,10 +1,10 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.3.2.0</token> + <token name="@WRAPPER_VERSION@">3.5.1.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.3.2">deeptools</requirement> + <requirement type="package" version="3.5.1">deeptools</requirement> <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" />
--- a/plotHeatmap.xml Sat Jan 25 05:15:40 2020 -0500 +++ b/plotHeatmap.xml Fri Feb 11 16:10:54 2022 +0000 @@ -34,6 +34,10 @@ --sortRegions '$advancedOpt.sortRegions' #end if + #if $advancedOpt.linesAtTickMarks: + --linesAtTickMarks + #end if + #if $advancedOpt.sortUsing: --sortUsing '$advancedOpt.sortUsing' #end if @@ -71,9 +75,15 @@ #if str($advancedOpt.yMin).strip() != "": --yMin $advancedOpt.yMin #end if - #if $advancedOpt.yMax: + #if str($advancedOpt.yMax).strip() != "": --yMax $advancedOpt.yMax #end if + #if str($advancedOpt.sortUsingSamples).strip() != "": + --sortUsingSamples $advancedOpt.sortUsingSamples + #end if + #if str($advancedOpt.clusterUsingSamples).strip() != "": + --clusterUsingSamples $advancedOpt.clusterUsingSamples + #end if --xAxisLabel '$advancedOpt.xAxisLabel' --yAxisLabel '$advancedOpt.yAxisLabel' @@ -130,6 +140,17 @@ <when value="yes"> <expand macro="sortRegions" /> <expand macro="sortUsing" /> + <param argument="--sortUsingSamples" type="text" + label="List of samples to be used for sorting" + help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting. + If no value is set, it uses all samples. Example: 1 3 (space separated!)" /> + <sanitizer> + <valid initial="string.printable"> + <add value=" "/> + </valid> + </sanitizer> + <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue="" + label="Draw dashed lines in heatmap above all tick marks?" /> <param argument="--averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap" help=""> @@ -162,19 +183,19 @@ help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must be between 0 and 1. A value of 0.0 would be fully transparent." /> - <param argument="--colorList" type="text" value="" size="50" optional="True" + <param argument="--colorList" type="text" value="" optional="True" label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas" help="The color of the heatmaps can be specified as a list of colors separated by comas with not space in between. For example: white,blue white,green will set a color map from white to blue for the first heatmap and for white to green for the next heatmap."/> <expand macro="zMin_zMax" /> - <param argument="--yMin" type="float" value="" size="3" optional="True" + <param argument="--yMin" type="float" value="" optional="True" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/> - <param argument="--yMax" type="float" value="" size="3" optional="True" + <param argument="--yMax" type="float" value="" optional="True" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/> - <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200" + <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" label="The x-axis label" help="" /> - <param argument="--yAxisLabel" type="text" value="genes" size="30" + <param argument="--yAxisLabel" type="text" value="genes" label="The y-axis label for the top panel" help="" /> <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100" @@ -189,17 +210,17 @@ <option value="heatmap and colorbar">heatmap and colorbar</option> </param> - <param argument="--startLabel" type="text" value="TSS" size="10" + <param argument="--startLabel" type="text" value="TSS" label="Label for the region start" help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start"." /> - <param argument="--endLabel" type="text" value="TES" size="10" + <param argument="--endLabel" type="text" value="TES" label="Label for the region end" help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/> - <param argument="--referencePointLabel" type="text" value="TSS" size="10" + <param argument="--referencePointLabel" type="text" value="TSS" label="Reference point label" help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. "peak start" etc." /> - <param argument="--samplesLabel" type="text" size="30" + <param argument="--samplesLabel" type="text" label="Labels for the samples (each bigwig) plotted" help="The default is to use the file name of the sample. The sample labels should be separated by spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> @@ -208,7 +229,7 @@ </valid> </sanitizer> </param> - <param argument="--regionsLabel" type="text" size="30" + <param argument="--regionsLabel" type="text" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by space is required. If a label itself contains a space, then quotes are needed. @@ -222,6 +243,15 @@ help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/> <expand macro="kmeans_clustering" /> + <param argument="--clusterUsingSamples" type="text" + label="List of samples to be used for clustering" + help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering. + If no value is set, it uses all samples. Example: 1 3 (space separated!)"/> + <sanitizer> + <valid initial="string.printable"> + <add value=" "/> + </valid> + </sanitizer> </when> </conditional> </inputs>
--- a/readme.rst Sat Jan 25 05:15:40 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -======================== -Galaxy deeptools wrapper -======================== - -deepTools are user-friendly tools for the normalization and visualization of -deep-sequencing data. -They address the challenge of visualizing the large amounts of data that are now -routinely generated from sequencing centers in a meaningful way. -To do so, deepTools contain useful routines to process the mapped reads data -through removal of duplicates and different filtering options to create coverage -files in standard bedGraph and bigWig file formats. deepTools allow the creation -of normalized coverage files or the comparison between two files -(for example, treatment and control). Finally, using such normalized and -standardized files, multiple visualizations can be created to identify -enrichments with functional annotations of the genome. -For a gallery of images that can be produced and a description -of the tools see our poster_. - -.. _poster: http://f1000.com/posters/browse/summary/1094053 - -deeptools is developed under here: - - https://github.com/deeptools/deepTools - -For support or questions please post to `Biostars <http://biostars.org>`__. For bug reports and feature requests please open an issue `<on github <http://github.com/deeptools/deeptools>`__. - - -============ -Installation -============ - -Requirements: python-2.7 - -Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. - -For the best performance we recommend to install blas/lapack/atlas in your environment before -installing deepTools from the Tool Shed. - - -======== -Citation -======== - -deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools. - - -======= -History -======= - - * v1.0: Initial public release - * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version - - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE.
--- a/repository_dependencies.xml Sat Jan 25 05:15:40 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0" ?> -<repositories> - <repository changeset_revision="16c0c73b28ad" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/> -</repositories> \ No newline at end of file
--- a/test-data/bamPEFragmentSize_result1.txt Sat Jan 25 05:15:40 2020 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Fri Feb 11 16:10:54 2022 +0000 @@ -12,7 +12,7 @@ Max.: 251.0 Std: 4.496912521077347 MAD: 1.0 -Len. 10%: 241.20000000000002 +Len. 10%: 241.2 Len. 20%: 241.4 Len. 30%: 241.6 Len. 40%: 241.8
--- a/test-data/bamPEFragmentSize_table1.txt Sat Jan 25 05:15:40 2020 -0500 +++ b/test-data/bamPEFragmentSize_table1.txt Fri Feb 11 16:10:54 2022 +0000 @@ -1,2 +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 +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
--- a/test-data/plotFingerprint_quality_metrics.tabular Sat Jan 25 05:15:40 2020 -0500 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Feb 11 16:10:54 2022 +0000 @@ -1,3 +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 NA 0.26900449806812143 NA NA NA -bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.26900449806812143 0 0 0 +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
--- a/test-data/plotPCA_result2.tabular Sat Jan 25 05:15:40 2020 -0500 +++ b/test-data/plotPCA_result2.tabular Fri Feb 11 16:10:54 2022 +0000 @@ -1,4 +1,4 @@ #plotPCA --outFileNameData Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue 1 -0.7071067811865476 -0.7071067811865475 4.0 -2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32 +2 -0.7071067811865475 0.7071067811865476 2.49319462166397e-32