| Next changeset 1:ef86780a77ff (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 hicCorrelate.xml hicFindEnrichedContacts.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 fe0243c46b36 _hicExport._xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_hicExport._xml Thu Mar 30 02:50:08 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 fe0243c46b36 hicCorrelate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicCorrelate.xml Thu Mar 30 02:50:08 2017 -0400 |
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| @@ -0,0 +1,94 @@ +<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0"> + <description>Computes pairwise correlations between hic matrices data</description> + <macros> + <token name="@BINARY@">hicCorrelate</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> +<![CDATA[ + + @multiple_input_matrices@ + hicCorrelate + + --matrices $matrices + --labels $mlabels + + #if $method and $method is not None: + --method $method + #end if + $log1p + + #if $use_range.select_use_range == "yes_use_range" + --range $range_min:$range_max + #end if + + #if $chromosomes: + --chromosomes #echo '" "'.join([ '"%s"' % $chrom for $chrom in $chromosomes ])# + #end if + + --colorMap $colormap + + --outFileNameHeatmap ./heatmap.png + --outFileNameScatter ./scatter.png +]]> + </command> + <inputs> + <expand macro="multiple_input_matrices" /> + + <param name="method" type="select" label="Correlation method to use" argument="--method" > + <option value="spearman">Spearman</option> + <option selected="true" value="pearson">Pearson</option> + </param> + <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue="" + label="Use the log1p of the matrix values" help="(--log1p)" /> + <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> + <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> + <option value="no_use_range">No restriction</option> + <option value="yes_use_range">Only consider counts within a range</option> + </param> + <when value="no_use_range"/> + <when value="yes_use_range"> + <param name="range_min" type="integer" value="" min="0"/> + <param name="range_max" type="integer" value="" min="0"/> + </when> + </conditional> + <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0"> + <param name="chromosome" type="text"/> + </repeat> + + <expand macro="colormap" /> + + </inputs> + <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so --> + <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" /> + <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" /> + </outputs> + <tests> + <test> + <repeat name="input_files"> + <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/> + <param name="mlabel" value="first"/> + </repeat> + <repeat name="input_files"> + <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" /> + <param name="mlabel" value="second"/> + </repeat> + <param name="log1p" value="True"/> + <param name="colormap" value="jet"/> + <param name="method" value="spearman"/> + <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/> + <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +Computes pairwise correlations between hic matrices data. +The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices. + + +]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fe0243c46b36 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 30 02:50:08 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 fe0243c46b36 test-data/domains.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/domains.bed Thu Mar 30 02:50:08 2017 -0400 |
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@@\n+#{"numberOfProcessors":1,"minDepth":20000,"matrix":"matrix.npz.h5","outFileName":"./tadScoreFile.tabular","binsize":5000,"step":100000,"command":"TAD_score","maxDepth":60000,"zscore_matrix":"./tadScoreFile.tabular_zscore_matrix.h5"}\n+chr2RHet\t0\t5000\t0.000000\n+chr2RHet\t5000\t10000\t-0.095120\n+chr2RHet\t10000\t15000\t-0.086382\n+chr2RHet\t15000\t20000\t-0.080500\n+chr2RHet\t20000\t25000\t-0.075802\n+chr2RHet\t25000\t30000\t0.847009\n+chr2RHet\t30000\t35000\t-0.075802\n+chr2RHet\t35000\t40000\t-0.075802\n+chr2RHet\t40000\t45000\t-0.075802\n+chr2RHet\t45000\t50000\t-0.075802\n+chr2RHet\t50000\t55000\t-0.075802\n+chr2RHet\t55000\t60000\t-0.075802\n+chr2RHet\t60000\t65000\t-0.075802\n+chr2RHet\t65000\t70000\t-0.075802\n+chr2RHet\t70000\t75000\t-0.075802\n+chr2RHet\t75000\t80000\t-0.075802\n+chr2RHet\t80000\t85000\t0.580227\n+chr2RHet\t85000\t90000\t0.580227\n+chr2RHet\t90000\t95000\t0.580227\n+chr2RHet\t95000\t100000\t0.339230\n+chr2RHet\t100000\t105000\t0.339230\n+chr2RHet\t105000\t110000\t-0.075802\n+chr2RHet\t110000\t115000\t-0.075802\n+chr2RHet\t115000\t120000\t-0.075802\n+chr2RHet\t120000\t125000\t1.054400\n+chr2RHet\t125000\t130000\t1.054400\n+chr2RHet\t130000\t135000\t-0.075802\n+chr2RHet\t135000\t140000\t-0.075802\n+chr2RHet\t140000\t145000\t0.339230\n+chr2RHet\t145000\t150000\t0.339230\n+chr2RHet\t150000\t155000\t-0.075802\n+chr2RHet\t155000\t160000\t-0.075802\n+chr2RHet\t160000\t165000\t-0.075802\n+chr2RHet\t165000\t170000\t-0.075802\n+chr2RHet\t170000\t175000\t-0.075802\n+chr2RHet\t175000\t180000\t-0.075802\n+chr2RHet\t180000\t185000\t-0.075802\n+chr2RHet\t185000\t190000\t-0.075802\n+chr2RHet\t190000\t195000\t-0.075802\n+chr2RHet\t195000\t200000\t0.328485\n+chr2RHet\t200000\t205000\t1.712156\n+chr2RHet\t205000\t210000\t1.712156\n+chr2RHet\t210000\t215000\t1.712156\n+chr2RHet\t215000\t220000\t1.056126\n+chr2RHet\t220000\t225000\t-0.075802\n+chr2RHet\t225000\t230000\t-0.075802\n+chr2RHet\t230000\t235000\t-0.075802\n+chr2RHet\t235000\t240000\t-0.075802\n+chr2RHet\t240000\t245000\t-0.075802\n+chr2RHet\t245000\t250000\t-0.075802\n+chr2RHet\t250000\t255000\t-0.075802\n+chr2RHet\t255000\t260000\t-0.075802\n+chr2RHet\t260000\t265000\t-0.075802\n+chr2RHet\t265000\t270000\t-0.075802\n+chr2RHet\t270000\t275000\t-0.075802\n+chr2RHet\t275000\t280000\t-0.075802\n+chr2RHet\t280000\t285000\t-0.075802\n+chr2RHet\t285000\t290000\t-0.075802\n+chr2RHet\t290000\t295000\t-0.075802\n+chr2RHet\t295000\t300000\t-0.075802\n+chr2RHet\t300000\t305000\t-0.075802\n+chr2RHet\t305000\t310000\t-0.075802\n+chr2RHet\t310000\t315000\t-0.075802\n+chr2RHet\t315000\t320000\t-0.075802\n+chr2RHet\t320000\t325000\t-0.075802\n+chr2RHet\t325000\t330000\t-0.075802\n+chr2RHet\t330000\t335000\t-0.075802\n+chr2RHet\t335000\t340000\t-0.075802\n+chr2RHet\t340000\t345000\t-0.075802\n+chr2RHet\t345000\t350000\t-0.075802\n+chr2RHet\t350000\t355000\t-0.075802\n+chr2RHet\t355000\t360000\t-0.075802\n+chr2RHet\t360000\t365000\t-0.075802\n+chr2RHet\t365000\t370000\t-0.075802\n+chr2RHet\t370000\t375000\t-0.075802\n+chr2RHet\t375000\t380000\t1.056126\n+chr2RHet\t380000\t385000\t1.056126\n+chr2RHet\t385000\t390000\t1.056126\n+chr2RHet\t390000\t395000\t1.056126\n+chr2RHet\t395000\t400000\t-0.075802\n+chr2RHet\t400000\t405000\t-0.075802\n+chr2RHet\t405000\t410000\t-0.075802\n+chr2RHet\t410000\t415000\t-0.075802\n+chr2RHet\t415000\t420000\t-0.075802\n+chr2RHet\t420000\t425000\t-0.075802\n+chr2RHet\t425000\t430000\t-0.075802\n+chr2RHet\t430000\t435000\t-0.075802\n+chr2RHet\t435000\t440000\t-0.075802\n+chr2RHet\t440000\t445000\t-0.075802\n+chr2RHet\t445000\t450000\t-0.075802\n+chr2RHet\t450000\t455000\t-0.075802\n+chr2RHet\t455000\t460000\t-0.075802\n+chr2RHet\t460000\t465000\t-0.075802\n+chr2RHet\t465000\t470000\t-0.075802\n+chr2RHet\t470000\t475000\t-0.075802\n+chr2RHet\t475000\t480000\t-0.075802\n+chr2RHet\t480000\t485000\t-0.075802\n+chr2RHet\t485000\t490000\t-0.075802\n+chr2RHet\t490000\t495000\t-0.075802\n+chr2RHet\t495000\t500000\t-0.075802\n+chr2RHet\t500000\t505000\t-0.075802\n+chr2RHet\t505000\t510000\t-0.075802\n+chr2RHet\t510000\t515000\t-0.075802\n+chr2RHet\t515000\t520000\t-0.075802\n+chr2RHet\t520000\t525000\t-0.075802\n+chr2RHet\t525000\t530000\t-0.075802\n+chr2RHet\t530000\t535000\t-0.075802\n+chr2RHet\t535000\t540000\t-0.075802\n+chr2RHet\t540000\t545000\t-0.075802\n+chr2RHet\t545000\t550000\t-0.075802\n+chr2RHet\t550000\t555000\t0.848419\n+chr2RHet\t555000\t560000\t1.504449\n+chr'..b'\n+chr3R\t27375000\t27380000\t-0.202334\n+chr3R\t27380000\t27385000\t-0.202334\n+chr3R\t27385000\t27390000\t-0.202334\n+chr3R\t27390000\t27395000\t-0.202334\n+chr3R\t27395000\t27400000\t0.199516\n+chr3R\t27400000\t27405000\t0.726185\n+chr3R\t27405000\t27410000\t1.190531\n+chr3R\t27410000\t27415000\t0.833625\n+chr3R\t27415000\t27420000\t-0.202334\n+chr3R\t27420000\t27425000\t-0.202334\n+chr3R\t27425000\t27430000\t0.368686\n+chr3R\t27430000\t27435000\t0.691346\n+chr3R\t27435000\t27440000\t0.691346\n+chr3R\t27440000\t27445000\t0.430560\n+chr3R\t27445000\t27450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|
| b |
| diff -r 000000000000 -r fe0243c46b36 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 02:50:08 2017 -0400 |
| b |
| b'@@ -0,0 +1,25245 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|
| b |
| diff -r 000000000000 -r fe0243c46b36 test-data/hicPlotDistVsCounts_result1.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result1.png has changed |
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| diff -r 000000000000 -r fe0243c46b36 test-data/hicPlotMatrix_result1.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicPlotMatrix_result1.svg Thu Mar 30 02:50:08 2017 -0400 |
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