Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix
comparison hicAdjustMatrix.xml @ 6:a7fd644deda6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:30:48 +0000 |
| parents | cc52e4ded146 |
| children | 2dccb6bb0add |
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| 5:794bd416f6c3 | 6:a7fd644deda6 |
|---|---|
| 1 <tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 2 <description>adjust the shape of a Hi-C matrix</description> | 2 <description>adjust the shape of a Hi-C matrix</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicAdjustMatrix</token> | 4 <token name="@BINARY@">hicAdjustMatrix</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 20 --chromosomes '$chroms' | 20 --chromosomes '$chroms' |
| 21 #end if | 21 #end if |
| 22 #end if | 22 #end if |
| 23 | 23 |
| 24 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile": | 24 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile": |
| 25 --regions '$chromosomeOrRegionFile_conditional.regions' | 25 --regions '$chromosomeOrRegionFile_conditional.regions' |
| 26 #end if | 26 #end if |
| 27 | 27 |
| 28 && mv "$matrix_file_out" matrix | 28 && mv '$matrix_file_out' matrix |
| 29 ]]> | 29 ]]> |
| 30 </command> | 30 </command> |
| 31 <inputs> | 31 <inputs> |
| 32 <expand macro='matrix_h5_cooler_macro' /> | 32 <expand macro='matrix_h5_cooler_macro' /> |
| 33 <param name="action_selector" type="select" label="Apply action" > | 33 <param name="action_selector" type="select" label="Apply action"> |
| 34 <option value="keep" selected="True">keep</option> | 34 <option value="keep" selected="True">keep</option> |
| 35 <option value="remove">remove</option> | 35 <option value="remove">remove</option> |
| 36 <option value="mask">mask</option> | 36 <option value="mask">mask</option> |
| 37 </param> | 37 </param> |
| 38 <conditional name="chromosomeOrRegionFile_conditional"> | 38 <conditional name="chromosomeOrRegionFile_conditional"> |
| 39 <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions"> | 39 <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
| 40 <option value="optionChromosomes">Chromosomes</option> | 40 <option value="optionChromosomes">Chromosomes</option> |
| 41 <option value="optionRegionFile" selected="True">Region BED file</option> | 41 <option value="optionRegionFile" selected="True">Region BED file</option> |
| 42 </param> | 42 </param> |
| 43 <when value="optionChromosomes"> | 43 <when value="optionChromosomes"> |
| 44 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" | 44 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" help="The selected option will be applied on the selected chromosomes."> |
| 45 help="The selected option will be applied on the selected chromosomes." > | 45 <param name="chromosome" type="text"> |
| 46 <param name="chromosome" type="text" > | |
| 47 <validator type="empty_field" /> | 46 <validator type="empty_field" /> |
| 48 </param> | 47 </param> |
| 49 </repeat> | 48 </repeat> |
| 50 | |
| 51 </when> | 49 </when> |
| 52 <when value="optionRegionFile"> | 50 <when value="optionRegionFile"> |
| 53 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered." | 51 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" 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 | |
| 56 </when> | 52 </when> |
| 57 </conditional> | 53 </conditional> |
| 58 </inputs> | 54 </inputs> |
| 59 <outputs> | 55 <outputs> |
| 60 <data name="outFileName" from_work_dir="matrix" format="h5"> | 56 <data name="outFileName" from_work_dir="matrix" format="h5"> |
| 61 <change_format> | 57 <change_format> |
| 62 <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> | 58 <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> |
| 63 </change_format> | 59 </change_format> |
| 64 </data> | 60 </data> |
| 65 </outputs> | 61 </outputs> |
| 66 <tests> | 62 <tests> |
| 67 <test> | 63 <test expect_num_outputs="1"> |
| 68 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> | 64 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> |
| 69 <param name="action_selector" value="keep" /> | 65 <param name="action_selector" value="keep" /> |
| 70 <conditional name="chromosomeOrRegionFile_conditional"> | 66 <conditional name="chromosomeOrRegionFile_conditional"> |
| 71 <param name="chromosomeOrRegionFile_selector" value='optionChromosomes'/> | 67 <param name="chromosomeOrRegionFile_selector" value='optionChromosomes' /> |
| 72 <repeat name="chromosomeOrder"> | 68 <repeat name="chromosomeOrder"> |
| 73 <param name="chromosome" value='chrX'/> | 69 <param name="chromosome" value='chrX' /> |
| 74 <param name="chromosome" value='chr3R'/> | 70 <param name="chromosome" value='chr3R' /> |
| 75 </repeat> | 71 </repeat> |
| 76 </conditional> | 72 </conditional> |
| 77 | |
| 78 <output name="outFileName" ftype="h5"> | 73 <output name="outFileName" ftype="h5"> |
| 79 <assert_contents> | 74 <assert_contents> |
| 80 <has_h5_keys keys='intervals,matrix'/> | 75 <has_h5_keys keys='intervals,matrix' /> |
| 81 </assert_contents> | 76 </assert_contents> |
| 82 </output> | 77 </output> |
| 83 </test> | 78 </test> |
| 84 | 79 <test expect_num_outputs="1"> |
| 85 <test> | 80 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> |
| 86 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> | |
| 87 <param name="action_selector" value="mask" /> | 81 <param name="action_selector" value="mask" /> |
| 88 <conditional name="chromosomeOrRegionFile_conditional"> | 82 <conditional name="chromosomeOrRegionFile_conditional"> |
| 89 <param name="chromosomeOrRegionFile_selector" value='optionRegionFile'/> | 83 <param name="chromosomeOrRegionFile_selector" value='optionRegionFile' /> |
| 90 <param name="regions" value='regions.bed'/> | 84 <param name="regions" value='regions.bed' /> |
| 91 </conditional> | 85 </conditional> |
| 92 | |
| 93 <output name="outFileName" ftype="h5"> | 86 <output name="outFileName" ftype="h5"> |
| 94 <assert_contents> | 87 <assert_contents> |
| 95 <has_h5_keys keys='intervals,matrix,nan_bins'/> | 88 <has_h5_keys keys='intervals,matrix,nan_bins' /> |
| 96 </assert_contents> | 89 </assert_contents> |
| 97 </output> | 90 </output> |
| 98 </test> | 91 </test> |
| 99 </tests> | 92 </tests> |
| 100 <help><![CDATA[ | 93 <help><![CDATA[ |
| 107 _________________ | 100 _________________ |
| 108 | 101 |
| 109 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | 102 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
| 110 | 103 |
| 111 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 104 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
| 112 ]]></help> | 105 ]]> </help> |
| 113 <expand macro="citations" /> | 106 <expand macro="citations" /> |
| 114 </tool> | 107 </tool> |