Mercurial > repos > bgruening > deeptools_compute_matrix
diff computeMatrix.xml @ 3:a842285199d9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
| author | bgruening |
|---|---|
| date | Wed, 09 Mar 2016 18:33:21 -0500 |
| parents | 275ed3e83de0 |
| children | aee77c22123d |
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--- a/computeMatrix.xml Thu Feb 18 11:53:52 2016 -0500 +++ b/computeMatrix.xml Wed Mar 09 18:33:21 2016 -0500 @@ -51,7 +51,12 @@ #if $mode.regionStartLength.regionStartLength_select == "yes": --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength + + --unscaled5prime $mode.regionStartLength.unscaled5prime + --unscaled3prime $mode.regionStartLength.unscaled3prime + #end if + #end if #if $advancedOpt.showAdvancedOpt == "yes": @@ -71,7 +76,6 @@ #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': --scale $advancedOpt.scale #end if - #end if ]]> </command> @@ -118,6 +122,14 @@ label="Distance downstream of the region end position" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> + <param argument="--unscaled5prime" type="integer" min="0" value="0" + label="Number of bases within the gene body at the 5-prime end to exclude from scaling." + help="By default, each region is scaled to a given length (see the --regionBodyLength + option). In some cases it is useful to look at unscaled signals around region boundaries, so this + setting specifies the number of unscaled bases on the 5-prime end of each boundary." /> + <param argument="--unscaled3prime" type="integer" min="0" value="0" + label="Number of bases within the gene body at the 3-prime end to exclude from scaling." + help="As with --unscaled5prime, but for the 3-prime end." /> </when> </conditional> </when> @@ -202,9 +214,6 @@ <expand macro="output_graphic_outputs" /> <expand macro="output_save_matrix_values" /> </outputs> - <!-- - computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 - --> <tests> <test> <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />