| Previous changeset 4:c4f273c3c73f (2018-04-27) Next changeset 6:6cca935297f6 (2019-12-16) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287 |
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modified:
hicPlotViewpoint.xml macros.xml test-data/Li_chrX30-35_cool.png test-data/Li_et_al_2015.cool |
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added:
test-data/distVsCounts.txt |
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| diff -r c4f273c3c73f -r 67bd57e960a3 hicPlotViewpoint.xml --- a/hicPlotViewpoint.xml Fri Apr 27 08:43:05 2018 -0400 +++ b/hicPlotViewpoint.xml Sat Jun 09 15:34:08 2018 -0400 |
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| @@ -7,18 +7,29 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - hicPlotViewpoint --matrix '$matrix_h5_cooler' + #for $counter, $m in enumerate($matrix_h5_cooler_multiple): + ln -s '$m' ${counter}_matrix && + #end for + #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ]) + + hicPlotViewpoint --matrix "$m" #if $interactionOutFileName: - $interactionOutFileName interactions.bedgraph + $interactionOutFileName interactions #end if --outFileName plot.$image_file_format --region $region --referencePoint $referencePoint && mv plot.$image_file_format plot + && ls -lah + #if $interactionOutFileName: + #for $counter, $m in enumerate($matrix_h5_cooler_multiple): + && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph + #end for + #end if ]]> </command> <inputs> - <expand macro='matrix_h5_cooler_macro' /> + <expand macro='matrix_h5_cooler_multiple_macro' /> <expand macro="region" /> <param name="referencePoint" type="text" label="Reference point" help="The format is chr:referencePoint or chr:regionStart-regionEnd."/> @@ -33,34 +44,37 @@ </inputs> <outputs> - <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> + <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: 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' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph"> + + <data format="bedgraph" name="interactionFile" > + <discover_datasets pattern='(?P<designation>.+)\_interactions\.bedgraph' directory="." visible="true"/> <filter>interactionOutFileName</filter> </data> </outputs> <tests> <test> - <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/> + <param name="matrix_h5_cooler_multiple" 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="matrix_h5_cooler_multiple" 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"/> - + <output name="interactionFile"> + <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" /> + </output> </test> </tests> <help><