| Next changeset 1:68e57be0d284 (2017-04-03) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 |
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added:
_hicExport._xml hicFindEnrichedContacts.xml hicPlotMatrix.xml involucro macros.xml test-data/Li_et_al_2015.h5 test-data/diagnostic_plot.png test-data/dm3_genes.bed.gz test-data/dm3_genes.bed6.gz test-data/domains.bed test-data/hicBuildMatrix_result1.bam test-data/hicBuildMatrix_result1.h5 test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicFindTADs_TAD_score.tabular test-data/hicFindTADs_find_boundaries.bed test-data/hicFindTADs_find_boundaries.gff test-data/hicFindTADs_find_domains.bed test-data/hicFindTADs_find_score.bedgraph test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotMatrix_result1.svg test-data/hicPlotTADs_result1.svg test-data/hicSumMatrices_result1.npz.h5 test-data/merged_matrix.npz.h5 test-data/small_test_R1_unsorted.bam test-data/small_test_R2_unsorted.bam test-data/small_test_matrix_50kb_res.h5 test-data/tadScoreFile.tabular_zscore_matrix.h5 test-data/tad_classification.bed test-data/tad_score.gz |
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| diff -r 000000000000 -r a9050bffb50c _hicExport._xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_hicExport._xml Thu Mar 30 02:12:31 2017 -0400 |
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| @@ -0,0 +1,55 @@ +<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 000000000000 -r a9050bffb50c hicPlotMatrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicPlotMatrix.xml Thu Mar 30 02:12:31 2017 -0400 |
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| @@ -0,0 +1,135 @@ +<tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> + <description>Plots a HiC matrix heatmap</description> + <macros> + <token name="@BINARY@">hicPlotMatrix</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> +<![CDATA[ + ln -s '$matrix' input_matrix.h5 && + + @BINARY@ + + --matrix input_matrix.h5 + + #if $title and $title is not None: + --title '$title' + #end if + + #if $scoreName and $scoreName is not None: + --scoreName '$scoreName' + #end if + + + --outFileName plot.svg + + $perChromosome + $clearMaskedBins + + --whatToShow $whatToShow.whatToShow_select + + + ## special: --chromosomeOrder is optional, but if given needs at least one argument + #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) + #if chroms + --chromosomeOrder '$chroms' + #end if + + #if $region: + --region '$region' + #end if + + #if $region2: + --region2 '$region2' + #end if + $log1p + $log + + #if $colormap: + --colorMap $colormap + #end if + + #if $vMin: + --vMin $vMin + #end if + + #if $vMax: + --vMax $vMax + #end if + + #if $whatToShow.whatToShow_select != 'heatmap': + #if $whatToShow.zMax: + --zMax $whatToShow.zMax + #end if + #end if + +]]> + </command> + <inputs> + <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/> + <param argument="--title" type="text" optional="true" label="Plot title"/> + <param argument="--scoreName" type="text" optional="true" label="Score name"/> + <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" + label="Plot per chromosome" + help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" /> + <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" + label="Remove masked bins from the matrix" /> + + <conditional name="whatToShow"> + <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D"> + <option value="both">Show both</option> + <option value="heatmap" selected="true">Only heatmap</option> + <option value="3D">Only 3D</option> + </param> + <when value="both"> + <expand macro="zMax" /> + </when> + <when value="3D"> + <expand macro="zMax" /> + </when> + <when value="heatmap"/> + </conditional> + + <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):" + help="This option overrides --region and --region2"> + <param name="chromosome" type="text" /> + </repeat> + + <param argument="--region" type="text" optional="True" label="Plot only this region" + help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> + <param argument="--region2" type="text" optional="True" label="Region two to plot" + help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/> + <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/> + <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/> + + <expand macro="colormap" /> + + <param argument="--vMin" type="float" optional="true" label="vMin"/> + <param argument="--vMax" type="float" optional="true" label="vMax"/> + + </inputs> + <outputs> + <data name="outFileName" from_work_dir="plot.svg" format="svg" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/> + <param name="region" value="chrX:3000000-3500000"/> + <param name="region2" value="chrX:3100000-3600000"/> + <param name="log1p" value="True"/> + <param name="clearMaskedBins" value="True"/> + <param name="whatToShow_select" value="heatmap"/> + <output name="outFileName" file="hicPlotMatrix_result1.svg" ftype="svg" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +Plots a HiC matrix heatmap. + +]]></help> + <expand macro="citations" /> +</tool> + |
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| diff -r 000000000000 -r a9050bffb50c involucro |
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| diff -r 000000000000 -r a9050bffb50c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 30 02:12:31 2017 -0400 |
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| b'@@ -0,0 +1,542 @@\n+<macros>\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ <regex match="EXception:" />\n+ <regex match="Traceback" />\n+ </stdio>\n+ </xml>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+ <token name="@WRAPPER_VERSION@">1.7.1</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="2.7.13">python</requirement>\n+ <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <expand macro="stdio" />\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.159780</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="zMax">\n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->\n+ </xml>\n+\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <option value="flag">flag</option>\n+ <option value="prism">prism</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="binary">binary</option>\n+ <option value="pink">pink</option>\n+ <option value="gray">gray</option>\n+ <option value="copper">copper</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdPu">RdPu</option>\n+ <option value="YlGn">YlGn</option'..b'="93260000" />\n+ </conditional>\n+ </xml>\n+\n+ <xml name="image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="missingDataAsZero">\n+ <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"\n+ label ="Treat missing data as zero"\n+ help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />\n+ </xml>\n+\n+ <xml name="input_save_matrix_values">\n+ <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>\n+ </xml>\n+\n+ <xml name="input_graphic_output_settings">\n+ <conditional name="output" >\n+ <param name="showOutputSettings" type="select" label="Show advanced output settings" >\n+ <option value="no" selected="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <yield />\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n+ <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."/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="input_image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="output_image_file_format">\n+ <data format="png" name="outFileName" label="${tool.name} image">\n+ <change_format>\n+ <when input="output.outFileFormat" value="pdf" format="pdf" />\n+ <when input="output.outFileFormat" value="svg" format="svg" />\n+ <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="emf" format="emf" />\n+ </change_format>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_save_matrix_values">\n+ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveMatrix\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_graphic_outputs">\n+ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveData\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveSortedRegions\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+\n+\n+</macros>\n' |
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| diff -r 000000000000 -r a9050bffb50c test-data/domains.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/domains.bed Thu Mar 30 02:12:31 2017 -0400 |
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|
| b |
| diff -r 000000000000 -r a9050bffb50c test-data/hicFindTADs_find_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicFindTADs_find_score.bedgraph Thu Mar 30 02:12:31 2017 -0400 |
| b |
| b'@@ -0,0 +1,25245 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|
| b |
| diff -r 000000000000 -r a9050bffb50c test-data/hicPlotDistVsCounts_result1.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result1.png has changed |
| b |
| diff -r 000000000000 -r a9050bffb50c test-data/hicPlotMatrix_result1.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicPlotMatrix_result1.svg Thu Mar 30 02:12:31 2017 -0400 |
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