| Previous changeset 1:72883c28fdcd (2017-04-03) Next changeset 3:f569cd2afecb (2017-11-27) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251 |
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modified:
hicFindTADs.xml macros.xml |
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added:
test-data/bedgraph_chrx_2e6_5e6.bg test-data/bigwig_chrx_2e6_5e6.bw test-data/find_TADs/multiBonferroni_boundaries.bed test-data/find_TADs/multiBonferroni_boundaries.gff test-data/find_TADs/multiBonferroni_domains.bed test-data/find_TADs/multiBonferroni_score.bedgraph test-data/find_TADs/multiBonferroni_tad_score.bm test-data/find_TADs/multiBonferroni_zscore_matrix.h5 test-data/find_TADs/multiFDR_boundaries.bed test-data/find_TADs/multiFDR_boundaries.gff test-data/find_TADs/multiFDR_domains.bed test-data/find_TADs/multiFDR_score.bedgraph test-data/find_TADs/multiFDR_tad_score.bm test-data/find_TADs/multiFDR_zscore_matrix.h5 test-data/find_TADs/multiNone_boundaries.bed test-data/find_TADs/multiNone_boundaries.gff test-data/find_TADs/multiNone_domains.bed test-data/find_TADs/multiNone_score.bedgraph test-data/find_TADs/multiNone_tad_score.bm test-data/find_TADs/multiNone_zscore_matrix.h5 test-data/hicMergeMatrixBins_result1.npz.h5 test-data/master_TADs_plot.png test-data/master_matrix_plot.png test-data/small_test_matrix.h5 test-data/small_test_matrix_result.bam test-data/small_test_matrix_result_sorted.bam |
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removed:
_hicExport._xml hicFindEnrichedContacts.xml test-data/hicBuildMatrix_result1.h5 test-data/hicPlotDistVsCounts_result1_.png test-data/hicPlotMatrix_result1.svg test-data/tadScoreFile.tabular_zscore_matrix.h5 |
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| diff -r 72883c28fdcd -r a9c1d76b90c4 _hicExport._xml --- a/_hicExport._xml Mon Apr 03 07:29:57 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -<tool id="hicExport" name="hicExport" version="1.0"> - <description>saves a HiC Matrix in text format</description> - <macros> - <token name="@BINARY@">hicExport</token> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <command><![CDATA[ - hicExport - #if $matrix and $matrix is not None: - --matrix $matrix - #end if - --outputFormat $outputFormat - $clearMaskedBins - --outFileName $output - - ]]></command> - <inputs> - <param label="Matrix to use" name="matrix" type="data" help="(--matrix)" /> - <param label="Output format" name="outputFormat" type="select" - help="There are two possibilities: "dekker" and "ren". - The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels. - The "ren" format is a list of tuples of the form chrom, bin_star, bin_end, values. (--outputFormat)"> - <option selected="true" value="dekker">Dekker (first column and first rows are labels)</option> - <option value="ren">Ren (chrom, bin_star, bin_end, values)</option> - </param> - <param name="clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" label="If set, masked bins are removed from the matrix" - help="Masked bins are those that do not have any values, mainly because they are repetitive regions of the genome (--clearMaskedBins)" /> - </inputs> - <outputs> - <data format="txt" name="output"/> - </outputs> - <tests> - <test> - <param name="matrix" value="hicBuildMatrix_result1.npz"/> - <param name="outputFormat" value="dekker"/> - <output name="output" file="hicExport_result1.txt" ftpye="txt"/> - </test> - <test> - <param name="matrix" value="hicBuildMatrix_result1.npz"/> - <param name="outputFormat" value="ren"/> - <param name="clearMaskedBins" value="True"/> - <output name="output" file="hicExport_result2.txt" ftpye="txt"/> - </test> - </tests> - <help><![CDATA[ - -**What it does** - -Saves a HiC Matrix in text format - - ]]></help> - <expand macro="citations" /> -</tool> - |
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| diff -r 72883c28fdcd -r a9c1d76b90c4 hicFindTADs.xml --- a/hicFindTADs.xml Mon Apr 03 07:29:57 2017 -0400 +++ b/hicFindTADs.xml Thu Nov 02 11:13:55 2017 -0400 |
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| b'@@ -5,133 +5,110 @@\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements" />\n- <command><![CDATA[\n- #if $mode.mode_selector == \'TAD_score\':\n- ln -s \'$mode.matrix\' matrix.npz.h5 &&\n- #end if\n-\n- #if $mode.mode_selector == \'find_TADs\':\n- ln -s \'$tad_score_zscore_matrix\' ./tadScoreFile.tabular_zscore_matrix.h5 &&\n- #end if\n-\n+ <command detect_errors="exit_code"><![CDATA[\n+ \n hicFindTADs\n- $mode.mode_selector\n+ --matrix \'$matrix\'\n+ \n+ --delta $delta\n \n- #if $mode.mode_selector == \'find_TADs\':\n- --tadScoreFile \'$tadScoreFile\'\n- --outPrefix galaxy_tad_prefix\n- ##--maxThreshold $mode.maxThreshold\n- --delta $mode.delta\n- --pvalue $mode.pvalue\n- #if $mode.minBoundaryDistance:\n- --minBoundaryDistance $mode.minBoundaryDistance\n+ #if $minBoundaryDistance:\n+ --minBoundaryDistance $minBoundaryDistance\n+ #end if\n+ --minDepth $minDepth\n+ --maxDepth $maxDepth\n+ --step $step\n+ #if $multiple_comparison_conditional.multiple_comparison_selector == \'fdr\':\n+ --correctForMultipleTesting fdr\n+ --threshold $multiple_comparison_conditional.threshold\n+ #elif $multiple_comparison_conditional.multiple_comparison_selector == \'bonferroni\':\n+ --correctForMultipleTesting bonferroni\n+ --threshold $multiple_comparison_conditional.threshold\n+ #else:\n+ --multipleComparisons None \n #end if\n \n- #else:\n- --matrix matrix.npz.h5\n- --maxDepth $mode.maxDepth\n- --minDepth $mode.minDepth\n- --outFileName ./tadScoreFile.tabular\n-\n- --step $mode.step\n- #end if\n-\n+ --numberOfProcessors @THREADS@\n+ --outPrefix galaxy_tad_prefix\n ]]></command>\n <inputs>\n-\n- <conditional name="mode">\n- <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">\n- <option value="find_TADs">find TADs</option>\n- <option value="TAD_score">TAD score</option>\n+ <param argument="--matrix" type="data" format="h5" label="Corrected Hi-C matrix to use for the computations"/>\n+ <param argument="--minDepth" type="integer" value="40000"\n+ label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."\n+ help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>\n+ <param argument="--maxDepth" type="integer" value="100000"\n+ label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."\n+ help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>\n+ <param argument="--step" type="integer" value="10000"\n+ label="Step size when moving from minDepth to maxDepth"\n+ help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]\n+ until it reaches maxDepth. For example, selecting step=10,000, minDepth=20,000\n+ and maxDepth=150,000 will compute TAD-scores for window sizes:\n+ 20,000, 30,000, 40,000, 70,000 and 100,000"/>\n+ <conditional name="multiple_comparison_conditional">\n+ <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections" >\n+ <option value="fdr" selected="True">False discovery rate</option>\n+ <option value="bonferroni">Bonferroni correction</option>\n+ '..b'"bedgraph"\n- label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores">\n- <filter>mode[\'mode_selector\'] == "find_TADs"</filter>\n- </data>\n+ label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores" />\n <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"\n- label="${tool.name} on ${on_string}: TAD domains">\n- <filter>mode[\'mode_selector\'] == "find_TADs"</filter>\n- </data>\n+ label="${tool.name} on ${on_string}: TAD domains" />\n <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"\n- format="bed" label="${tool.name} on ${on_string}: Boundary information plus score">\n- <filter>mode[\'mode_selector\'] == "find_TADs"</filter>\n- </data>\n+ format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" />\n+ \n+ <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm"\n+ format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file" />\n+\n+ <data name="matrix_output" from_work_dir="galaxy_tad_prefix_zscore_matrix.h5"\n+ format="h5" label="${tool.name} on ${on_string}: Z-score matrix in h5" />\n </outputs>\n <tests>\n- <!--test>\n- <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>\n- <param name="mode_selector" value="TAD_score"/>\n- <param name="minDepth" value="20000"/>\n- <param name="maxDepth" value="60000"/>\n- <param name="step" value="100000"/>\n- <output name="outFileName" file="hicFindTADs_TAD_score.tabular" ftype="tabular"/>\n- <output name="tad_score_zscore_matrix" file="tadScoreFile.tabular_zscore_matrix.h5" ftype="h5" compare="sim_size"/>\n+ <test>\n+ <param name="matrix" value="small_test_matrix.h5" ftype="h5" />\n+ <param name="minDepth" value="60000"/>\n+ <param name="maxDepth" value="180000"/>\n+ <param name="step" value="20000"/>\n+ <param name="minBoundaryDistance" value="20000" />\n+ <conditional name="multiple_comparison_conditional">\n+ <param name="multiple_comparison_selector" value="fdr"/>\n+ <param name="threshold" value="0.1" />\n+ </conditional>\n+ <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" compare="sim_size" delta="35000" />\n+ <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" />\n+ <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" />\n+ <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" />\n+ <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" />\n+ <output name="matrix_output" file="find_TADs/multiFDR_zscore_matrix.h5" ftype="h5" compare="sim_size" delta="50000" />\n </test>\n- <test>\n- <param name="tadScoreFile" value="hicFindTADs_TAD_score.tabular" ftype="tabular"/>\n- <param name="tad_score_zscore_matrix" value="tadScoreFile.tabular_zscore_matrix.h5" ftype="h5"/>\n- <param name="mode_selector" value="find_TADs"/>\n- <param name="delta" value="0.002"/>\n- <param name="pvalue" value="0.01"/>\n-\n- <output name="boundaries" file="hicFindTADs_find_boundaries.bed" ftype="bed"/>\n- <output name="score" file="hicFindTADs_find_score.bedgraph" ftype="bedgraph"/>\n- <output name="domains" file="hicFindTADs_find_domains.bed" ftype="bed"/>\n- <output name="boundaries_bin" file="hicFindTADs_find_boundaries.gff" ftype="gff"/>\n- </test-->\n </tests>\n <help><
