Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts
diff hicPlotDistVsCounts.xml @ 11:4a3ccb7d4fc9 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
| author | iuc |
|---|---|
| date | Wed, 02 May 2018 16:48:34 -0400 |
| parents | b6fbf07de5af |
| children | 1beec69e6111 |
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--- a/hicPlotDistVsCounts.xml Fri Apr 27 08:29:56 2018 -0400 +++ b/hicPlotDistVsCounts.xml Wed May 02 16:48:34 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>compute distance vs Hi-C counts plot per chromosome</description> <macros> <token name="@BINARY@">hicPlotDistVsCounts</token> @@ -30,6 +30,10 @@ #if $chromosomeExclude: --chromosomeExclude '$chroms' #end if + + #if $outFileData_Boolean: + $outFileData_Boolean ./outFileData + #end if ]]> </command> <inputs> @@ -49,9 +53,14 @@ <validator type="empty_field" /> </param> </repeat> + <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM" + help="A bam file containing all data underlying the plots is saved on this file."/> </inputs> <outputs> <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/> + <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}"> + <filter>outFileData_Boolean</filter> + </data> </outputs> <tests> <test> @@ -60,6 +69,13 @@ <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"/> + <param name="skipDiagonal" value="False"/> + <param name='outFileData_Boolean' value='True'/> + <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/> + <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/> + </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" />