Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts
view hicPlotDistVsCounts.xml @ 7:ea39c587161f draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author | iuc |
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date | Wed, 07 Mar 2018 03:25:15 -0500 |
parents | 819bd2c44d4a |
children | 62803bb47880 |
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<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0"> <description>distance vs HiC counts plot per chromosome</description> <macros> <token name="@BINARY@">hicPlotDistVsCounts</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="aggressive"><![CDATA[ #import re #set matrices_path=[] #set matrices_labels=[] #for $counter, $m, in enumerate($matrices): #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier)) ln -f -s '${m}' '${identifier}_${counter}' && #silent $matrices_path.append("'%s_%s'" % ($identifier, $counter)) #silent $matrices_labels.append("'%s'" % ($identifier)) #end for @BINARY@ --matrices #echo " ".join($matrices_path)# --labels #echo " ".join($matrices_labels)# $skipDiagonal --plotFile plot.png #if $plotsize: --plotsize $plotsize #end if --maxdepth $maxdepth $perchr #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ]) #if $chromosomeExclude: --chromosomeExclude '$chroms' #end if ]]> </command> <inputs> <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="HiC normalized (corrected) matrices"/> <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" /> <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." /> <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." /> <param argument="--plotsize" type="text" optional="True" label="Plot size" help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." /> <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" help="This is useful for example to exclude the Y chromosome."> <param argument="--chromosomeExclude" type="text" value="" > <validator type="empty_field" /> </param> </repeat> </inputs> <outputs> <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test> <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/> <param name="skipDiagonal" value="False"/> <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/> </test> <test> <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/> <param name="skipDiagonal" value="False"/> <param name="perchr" value="True" /> <repeat name="chromosomeExclude"> <param name="chromosomeExclude" value="chrUextra"/> </repeat> <repeat name="chromosomeExclude"> <param name="chromosomeExclude" value="chrM"/> </repeat> <repeat name="chromosomeExclude"> <param name="chromosomeExclude" value="chr3LHet"/> </repeat> <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/> </test> </tests> <help><![CDATA[ Relation of genomic distance and number of contacts ======================================================== | This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare | them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case | of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple | matrices denser matrices are scaled down to match the sum of the smaller matrix. | | For more information about HiCExplorer please consider our documentation on readthedocs.io_ Input ----- Parameters __________ - contact matrix - skip diagonal - per chromosome - max depth - plot size - chromosome(s) to exclude Output ------- Output if all data in the contact matrix is considered: .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png :width: 70% Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome: .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png :width: 80% .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html ]]></help> <expand macro="citations" /> </tool>