Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix
comparison hicAdjustMatrix.xml @ 2:cc52e4ded146 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
| author | iuc |
|---|---|
| date | Wed, 11 Mar 2020 18:15:32 -0400 |
| parents | ea297a9c6f11 |
| children | a7fd644deda6 |
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| 1:ea297a9c6f11 | 2:cc52e4ded146 |
|---|---|
| 9 #set matrix_name = 'matrix_in.' + str($matrix_h5_cooler.ext) | 9 #set matrix_name = 'matrix_in.' + str($matrix_h5_cooler.ext) |
| 10 #set matrix_file_out = 'matrix_out.' + str($matrix_h5_cooler.ext) | 10 #set matrix_file_out = 'matrix_out.' + str($matrix_h5_cooler.ext) |
| 11 | 11 |
| 12 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && | 12 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && |
| 13 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' | 13 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' |
| 14 --action $action_selector | 14 --action $action_selector |
| 15 --outFileName '$matrix_file_out' | 15 --outFileName '$matrix_file_out' |
| 16 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionChromosomes": | 16 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionChromosomes": |
| 17 ## special: --chromosomeOrder is optional, but if given it needs at least one argument | 17 ## special: --chromosomeOrder is optional, but if given it needs at least one argument |
| 18 #set chroms = '\' \''.join([ str($var.chromosome) for $var in $chromosomeOrRegionFile_conditional.chromosomeOrder ]) | 18 #set chroms = '\' \''.join([ str($var.chromosome) for $var in $chromosomeOrRegionFile_conditional.chromosomeOrder ]) |
| 19 #if chroms: | 19 #if chroms: |
| 45 help="The selected option will be applied on the selected chromosomes." > | 45 help="The selected option will be applied on the selected chromosomes." > |
| 46 <param name="chromosome" type="text" > | 46 <param name="chromosome" type="text" > |
| 47 <validator type="empty_field" /> | 47 <validator type="empty_field" /> |
| 48 </param> | 48 </param> |
| 49 </repeat> | 49 </repeat> |
| 50 | 50 |
| 51 </when> | 51 </when> |
| 52 <when value="optionRegionFile"> | 52 <when value="optionRegionFile"> |
| 53 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered." | 53 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered." |
| 54 help="Should contain the regions which should be kept, removed or masked." /> | 54 help="Should contain the regions which should be kept, removed or masked." /> |
| 55 | 55 |
| 56 </when> | 56 </when> |
| 57 </conditional> | 57 </conditional> |
| 58 </inputs> | 58 </inputs> |
| 59 <outputs> | 59 <outputs> |
| 60 <data name="outFileName" from_work_dir="matrix" format="h5"> | 60 <data name="outFileName" from_work_dir="matrix" format="h5"> |
| 100 <help><![CDATA[ | 100 <help><![CDATA[ |
| 101 | 101 |
| 102 Adjust of the Hi-C matrix | 102 Adjust of the Hi-C matrix |
| 103 ========================= | 103 ========================= |
| 104 | 104 |
| 105 This tool is able to remove, keep or mask given regions of a Hi-C interaction matrix. | 105 This tool is able to remove, keep or mask given regions of a Hi-C interaction matrix, including entire chromosomes. |
| 106 | 106 |
| 107 _________________ | 107 _________________ |
| 108 | 108 |
| 109 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | 109 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
| 110 | 110 |