Mercurial > repos > bgruening > hicexplorer_hicaverageregions
comparison hicAverageRegions.xml @ 6:03d7978293fe draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 14:57:51 +0000 |
| parents | 4b6a36c18e5e |
| children | b15d27c440fd |
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| 5:2818b428a5c5 | 6:03d7978293fe |
|---|---|
| 1 <tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 2 <description>sums Hi-C contacts around given reference points and computes their average.</description> | 2 <description>sums Hi-C contacts around given reference points and computes their average.</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">hicAverageRegions</token> | 4 <token name="@BINARY@">hicAverageRegions</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 | |
| 10 | 9 |
| 11 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && | 10 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && |
| 12 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' | 11 @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext' |
| 13 | 12 |
| 14 --regions '$regions' | 13 --regions '$regions' |
| 22 | 21 |
| 23 ]]> | 22 ]]> |
| 24 </command> | 23 </command> |
| 25 <inputs> | 24 <inputs> |
| 26 <expand macro='matrix_h5_cooler_macro' /> | 25 <expand macro='matrix_h5_cooler_macro' /> |
| 27 <param argument="--regions" type="data" format='bed' | 26 <param argument="--regions" type="data" format='bed' label="Regions to average" help="BED file which stores a list of regions that are summed and averaged." /> |
| 28 label="Regions to average" | |
| 29 help="BED file which stores a list of regions that are summed and averaged."/> | |
| 30 | 27 |
| 31 <conditional name="rangeFormat_conditional"> | 28 <conditional name="rangeFormat_conditional"> |
| 32 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> | 29 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
| 33 <option value="optionGenomicUnits">Range in genomic units</option> | 30 <option value="optionGenomicUnits">Range in genomic units</option> |
| 34 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> | 31 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> |
| 35 </param> | 32 </param> |
| 36 <when value="optionGenomicUnits"> | 33 <when value="optionGenomicUnits"> |
| 37 <param name="upstreamRange" type="integer" value="" label="Upstream range"/> | 34 <param name="upstreamRange" type="integer" value="" label="Upstream range" /> |
| 38 <param name="downstreamRange" type="integer" value="" label="Downstream range"/> | 35 <param name="downstreamRange" type="integer" value="" label="Downstream range" /> |
| 39 </when> | 36 </when> |
| 40 <when value="optionBinUnits"> | 37 <when value="optionBinUnits"> |
| 41 <param name="upstreamRange" type="integer" value="" label="Upstream range"/> | 38 <param name="upstreamRange" type="integer" value="" label="Upstream range" /> |
| 42 <param name="downstreamRange" type="integer" value="" label="Downstream range"/> | 39 <param name="downstreamRange" type="integer" value="" label="Downstream range" /> |
| 43 </when> | 40 </when> |
| 44 </conditional> | 41 </conditional> |
| 45 <param name="coordinatesToBinMapping_selector" type="select" label="Define start value of range" help="If the region contains start and end coordinates, define if the start, center (start + (end-start) / 2) or end bin should be used as start for range."> | 42 <param name="coordinatesToBinMapping_selector" type="select" label="Define start value of range" help="If the region contains start and end coordinates, define if the start, center (start + (end-start) / 2) or end bin should be used as start for range."> |
| 46 <option value="start">Start</option> | 43 <option value="start">Start</option> |
| 47 <option value="center" selected="True">Center</option> | 44 <option value="center" selected="True">Center</option> |
| 48 <option value="end" selected="True">End</option> | 45 <option value="end" selected="True">End</option> |
| 49 </param> | 46 </param> |
| 50 </inputs> | 47 </inputs> |
| 51 <outputs> | 48 <outputs> |
| 52 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip"/> | 49 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip" /> |
| 53 </outputs> | 50 </outputs> |
| 54 <tests> | 51 <tests> |
| 55 <test> | 52 <test> |
| 56 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> | 53 <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> |
| 57 <param name="regions" value="hicAverageRegions/regions.bed" /> | 54 <param name="regions" value="hicAverageRegions/regions.bed" /> |
| 58 <conditional name="rangeFormat_conditional"> | 55 <conditional name="rangeFormat_conditional"> |
| 59 <param name="rangeFormat_selector" value='optionGenomicUnits'/> | 56 <param name="rangeFormat_selector" value='optionGenomicUnits' /> |
| 60 <param name="upstreamRange" value='100000'/> | 57 <param name="upstreamRange" value='100000' /> |
| 61 <param name="downstreamRange" value='100000'/> | 58 <param name="downstreamRange" value='100000' /> |
| 62 </conditional> | 59 </conditional> |
| 63 | 60 <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" /> |
| 64 <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" /> | |
| 65 </test> | 61 </test> |
| 66 <test> | 62 <test> |
| 67 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> | 63 <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> |
| 68 <param name="regions" value="hicAverageRegions/regions.bed" /> | 64 <param name="regions" value="hicAverageRegions/regions.bed" /> |
| 69 <conditional name="rangeFormat_conditional"> | 65 <conditional name="rangeFormat_conditional"> |
| 70 <param name="rangeFormat_selector" value='optionBinUnits'/> | 66 <param name="rangeFormat_selector" value='optionBinUnits' /> |
| 71 <param name="upstreamRange" value='100'/> | 67 <param name="upstreamRange" value='100' /> |
| 72 <param name="downstreamRange" value='100'/> | 68 <param name="downstreamRange" value='100' /> |
| 73 </conditional> | 69 </conditional> |
| 74 | 70 <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" /> |
| 75 <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" /> | |
| 76 </test> | 71 </test> |
| 77 </tests> | 72 </tests> |
| 78 <help><![CDATA[ | 73 <help><![CDATA[ |
| 79 | 74 |
| 80 Average regions | 75 Average regions |
| 89 _________________ | 84 _________________ |
| 90 | 85 |
| 91 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | 86 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
| 92 | 87 |
| 93 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 88 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
| 94 ]]></help> | 89 ]]> </help> |
| 95 <expand macro="citations" /> | 90 <expand macro="citations" /> |
| 96 </tool> | 91 </tool> |