Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint
diff hicPlotViewpoint.xml @ 0:58d146c74d72 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author | bgruening |
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date | Sat, 30 Dec 2017 09:11:56 -0500 |
parents | |
children | 745e77f4e81e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicPlotViewpoint.xml Sat Dec 30 09:11:56 2017 -0500 @@ -0,0 +1,88 @@ +<tool id="hicexplorer_hicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0"> + <description>computes the principal components for A / B compartment analysis</description> + <macros> + <token name="@BINARY@">hicPlotViewpoint</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + hicPlotViewpoint --matrix '$matrix_h5_cooler' + #if $interactionOutFileName: + $interactionOutFileName interactions.bedgraph + #end if + --outFileName plot.$image_file_format + --region $region + --referencePoint $referencePoint + && mv plot.$image_file_format plot +]]> + </command> + <inputs> + <expand macro='matrix_h5_cooler_macro' /> + <expand macro="region" /> + <param name="referencePoint" type="text" label="Reference point" + help="The format is chr:referencePoint or chr:regionStart-regionEnd."/> + + <param name="interactionOutFileName" type="boolean" truevalue="--interactionOutFileName" falsevalue="" checked="false" + label="Create bedgraph file with interactions" /> + <param name="image_file_format" type="select" label="Image output format"> + <option value="png">png</option> + <option value="svg">svg</option> + </param> + + </inputs> + <outputs> + + <data format="png" name="outFileName" from_work_dir="plot"> + <change_format> + <when input="image_file_format" value="png" format="png" /> + <when input="image_file_format" value="svg" format="svg" /> + </change_format> + </data> + <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph'> + <filter>interactionOutFileName</filter> + </data> + + </outputs> + <tests> + <test> + <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> + <param name="image_file_format" value="png" /> + <param name='region' value='X:3000000-3500000' /> + <param name='referencePoint' value='X:3200000' /> + <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/> + </test> + <test> + <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> + <param name="image_file_format" value="png" /> + <param name='region' value='X:3000000-3500000' /> + <param name='referencePoint' value='X:3200000-3300000' /> + <param name='interactionOutFileName' value='True' /> + <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/> + <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/> + + </test> + </tests> + <help><![CDATA[ +Principal component analysis +============================ +`hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis. + +Input +----- +- the matrix to be analysed + +Parameters +__________ +- Output file format: bigwig or bedgraph + +Output +------ +Two files with the first and the second eigenvector. + +| For more information about HiCExplorer please consider our documentation on readthedocs.io_ + +.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html +]]></help> + <expand macro="citations" /> +</tool>