Mercurial > repos > bgruening > deeptools_bam_compare
changeset 40:ce70d3cdf5d1 draft
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"
| author | bgruening |
|---|---|
| date | Fri, 11 Feb 2022 10:37:28 +0000 (2022-02-11) |
| parents | 64a7b4fc178a |
| children | c4ef24dfcfa1 |
| files | datatypes_conf.xml deepTools_macros.xml readme.rst repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/bamPEFragmentSize_table1.txt test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/plotCoverage.metrics test-data/plotCoverage_result1.png test-data/plotFingerprint_quality_metrics.tabular test-data/plotPCA_result2.tabular |
| diffstat | 12 files changed, 64 insertions(+), 19 deletions(-) [+] |
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--- a/datatypes_conf.xml Tue Apr 02 07:12:02 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <registration> - <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> - <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> - </registration> -</datatypes>
--- a/deepTools_macros.xml Tue Apr 02 07:12:02 2019 -0400 +++ b/deepTools_macros.xml Fri Feb 11 10:37:28 2022 +0000 @@ -1,10 +1,10 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.2.1.0</token> + <token name="@WRAPPER_VERSION@">3.5.1.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.2.1">deeptools</requirement> + <requirement type="package" version="3.5.1">deeptools</requirement> <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" /> @@ -164,6 +164,12 @@ </when> <when value="none" /> </conditional> + <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue="" + label="Compute the silhouette score for each region" + help="Compute the silhouette score for regions. This is only applicable if clustering has been performed. + The silhouette score is a measure of how similar a region is to other regions in the same cluster as + opposed to those in other clusters. It will be reported in the final column of the BED file with regions. + The silhouette evaluation can be very slow when you have more than 100 000 regions." /> </when> <when value="yes" /> </conditional> @@ -181,6 +187,7 @@ --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust #end if #end if + $advancedOpt.used_multiple_regions.silhouette #end if </token> @@ -217,10 +224,10 @@ help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." /> <param argument="--transcriptID" optional="True" value="transcript" type="text" label="transcript designator" - help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" /> + help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" /> <param argument="--exonID" optional="True" value="exon" type="text" label="exon designator" - help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" /> + help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" /> <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" label="transcriptID key designator" help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists) @@ -368,10 +375,12 @@ 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 +For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_. This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. +.. _Biostars: http://biostars.org +.. _on github: http://github.com .. _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/ @@ -824,6 +833,23 @@ <option value="brg">brg</option> <option value="jet">jet</option> <option value="afmhot">afmhot</option> + <option value="Wistia">Wistia</option> + <option value="cividis">cividis</option> + <option value="icefire">icefire</option> + <option value="inferno">inferno</option> + <option value="magma">magma</option> + <option value="mako">mako</option> + <option value="nipy_spectral">nipy_spectral</option> + <option value="plasma">plasma</option> + <option value="rocket">rocket</option> + <option value="tab10">tab10</option> + <option value="tab20">tab20</option> + <option value="tab20b">tab20b</option> + <option value="tab20c">tab20c</option> + <option value="twilight">twilight</option> + <option value="twilight_shifted">twilight_shifted</option> + <option value="viridis">viridis</option> + <option value="vlag">vlag</option> <option value="Accent_r">Accent reversed</option> <option value="Spectral_r">Spectral reversed</option> <option value="Set1_r">Set1 reversed</option> @@ -893,6 +919,23 @@ <option value="brg_r">brg reversed</option> <option value="jet_r">jet reversed</option> <option value="afmhot_r">afmhot reversed</option> + <option value="Wistia_r">Wistia reversed</option> + <option value="cividis_r">cividis reversed</option> + <option value="icefire_r">icefire reversed</option> + <option value="inferno_r">inferno reversed</option> + <option value="magma_r">magma reversed</option> + <option value="mako_r">mako reversed</option> + <option value="nipy_spectral_r">nipy_spectral reversed</option> + <option value="plasma_r">plasma reversed</option> + <option value="rocket_r">rocket reversed</option> + <option value="tab10_r">tab10 reversed</option> + <option value="tab20_r">tab20 reversed</option> + <option value="tab20b_r">tab20b reversed</option> + <option value="tab20c_r">tab20c reversed</option> + <option value="twilight_r">twilight reversed</option> + <option value="twilight_shifted_r">twilight_shifted reversed</option> + <option value="viridis_r">viridis reversed</option> + <option value="vlag_r">vlag reversed</option> </param> </xml>
--- a/readme.rst Tue Apr 02 07:12:02 2019 -0400 +++ b/readme.rst Fri Feb 11 10:37:28 2022 +0000 @@ -22,7 +22,7 @@ https://github.com/deeptools/deepTools -For support, questions, or feature requests contact: deeptools@googlegroups.com +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>`__. ============
--- a/repository_dependencies.xml Tue Apr 02 07:12:02 2019 -0400 +++ b/repository_dependencies.xml Fri Feb 11 10:37:28 2022 +0000 @@ -1,4 +1,4 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/> + <repository name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="b640d79b49cb"/> </repositories> \ No newline at end of file
--- a/test-data/bamPEFragmentSize_result1.txt Tue Apr 02 07:12:02 2019 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Fri Feb 11 10:37:28 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 Tue Apr 02 07:12:02 2019 -0400 +++ b/test-data/bamPEFragmentSize_table1.txt Fri Feb 11 10:37:28 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotCoverage.metrics Fri Feb 11 10:37:28 2022 +0000 @@ -0,0 +1,9 @@ +Sample Threshold Percent +bowtie2 test1.bam 0 100.000 +bowtie2 test1.bam 0 100.000 +bowtie2 test1.bam 5 1.509 +bowtie2 test1.bam 5 1.509 +bowtie2 test1.bam 10 1.461 +bowtie2 test1.bam 10 1.461 +bowtie2 test1.bam 20 1.406 +bowtie2 test1.bam 20 1.406
--- a/test-data/plotFingerprint_quality_metrics.tabular Tue Apr 02 07:12:02 2019 -0400 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Feb 11 10:37:28 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 Tue Apr 02 07:12:02 2019 -0400 +++ b/test-data/plotPCA_result2.tabular Fri Feb 11 10:37:28 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