Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts
diff hicPlotDistVsCounts.xml @ 2:3928cf4921b1 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
| author | iuc |
|---|---|
| date | Thu, 02 Nov 2017 10:53:09 -0400 |
| parents | 0ef2a42eca43 |
| children | fd133bb2ed84 |
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--- 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><![CDATA[ **What it does** -This program makes a distance vs. hi-c counts plots. It can use several matrix files to compare +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.