Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts
changeset 2:3928cf4921b1 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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--- a/_hicExport._xml Mon Apr 03 06:19:01 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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> -
--- a/hicPlotDistVsCounts.xml Mon Apr 03 06:19:01 2017 -0400 +++ b/hicPlotDistVsCounts.xml Thu Nov 02 10:53:09 2017 -0400 @@ -28,7 +28,7 @@ $perchr #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ]) #if $chromosomeExclude: - --chromosomeExclude $chroms + --chromosomeExclude '$chroms' #end if ]]> </command> @@ -44,7 +44,9 @@ 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="" /> + <param argument="--chromosomeExclude" type="text" value="" > + <validator type="empty_field" /> + </param> </repeat> </inputs> @@ -70,14 +72,14 @@ <repeat name="chromosomeExclude"> <param name="chromosomeExclude" value="chr3LHet"/> </repeat> - <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="15000"/> + <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/> </test> </tests> <help><