Mercurial > repos > bgruening > hicexplorer_hicaverageregions

comparison hicAverageRegions.xml @ 8:c72fa6cb8817 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 11:10:09 +0000
parents b15d27c440fd
children
comparison
equal deleted inserted replaced
7:b15d27c440fd 8:c72fa6cb8817
15 --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' 15 --range '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
16 #else: 16 #else:
17 --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange' 17 --rangeInBins '$rangeFormat_conditional.upstreamRange' '$rangeFormat_conditional.downstreamRange'
18 #end if 18 #end if
19 --coordinatesToBinMapping $coordinatesToBinMapping_selector 19 --coordinatesToBinMapping $coordinatesToBinMapping_selector
20 $considerStrandDirection
20 --outFileName output_matrix.npz 21 --outFileName output_matrix.npz
21 22
22 ]]> 23 ]]>
23 </command> 24 </command>
24 <inputs> 25 <inputs>
25 <expand macro='matrix_h5_cooler_macro' /> 26 <expand macro="matrix_h5_cooler_macro" />
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." /> 27 <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." />
27 28
28 <conditional name="rangeFormat_conditional"> 29 <conditional name="rangeFormat_conditional">
29 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions"> 30 <param name="rangeFormat_selector" type="select" label="List of chromosomes or a BED file containg regions">
30 <option value="optionGenomicUnits">Range in genomic units</option> 31 <option value="optionGenomicUnits">Range in genomic units</option>
31 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option> 32 <option value="optionBinUnits" selected="True">Range in bin (matrix indices) units</option>
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."> 43 <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.">
43 <option value="start">Start</option> 44 <option value="start">Start</option>
44 <option value="center" selected="True">Center</option> 45 <option value="center" selected="True">Center</option>
45 <option value="end" selected="True">End</option> 46 <option value="end" selected="True">End</option>
46 </param> 47 </param>
48 <param argument="--considerStrandDirection" type="boolean" truevalue="--considerStrandDirection" falsevalue="" label="Consider strand direction" help="This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1]." />
49
47 </inputs> 50 </inputs>
48 <outputs> 51 <outputs>
49 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip" /> 52 <data name="outFileName" from_work_dir="output_matrix.npz" format="zip" />
50 </outputs> 53 </outputs>
51 <tests> 54 <tests>
52 <test> 55 <test>
53 <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> 56 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
54 <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed"/> 57 <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed"/>
55 <conditional name="rangeFormat_conditional"> 58 <conditional name="rangeFormat_conditional">
56 <param name="rangeFormat_selector" value='optionGenomicUnits' /> 59 <param name="rangeFormat_selector" value="optionGenomicUnits" />
57 <param name="upstreamRange" value='100000' /> 60 <param name="upstreamRange" value="100000" />
58 <param name="downstreamRange" value='100000' /> 61 <param name="downstreamRange" value="100000" />
59 </conditional> 62 </conditional>
60 <output name='outFileName' file='hicAverageRegions/result_range_100000.npz' ftype="zip" compare="sim_size" delta="20000" /> 63 <output name="outFileName" file="hicAverageRegions/result_range_100000.npz" ftype="zip" compare="sim_size" delta="20000" />
61 </test> 64 </test>
62 <test> 65 <test>
63 <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> 66 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
64 <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed" /> 67 <param name="regions" value="hicAverageRegions/regions.bed" ftype="bed" />
65 <conditional name="rangeFormat_conditional"> 68 <conditional name="rangeFormat_conditional">
66 <param name="rangeFormat_selector" value='optionBinUnits' /> 69 <param name="rangeFormat_selector" value="optionBinUnits" />
67 <param name="upstreamRange" value='100' /> 70 <param name="upstreamRange" value="100" />
68 <param name="downstreamRange" value='100' /> 71 <param name="downstreamRange" value="100" />
69 </conditional> 72 </conditional>
70 <output name='outFileName' file='hicAverageRegions/result_rangeInBins_100.npz' ftype="zip" compare="sim_size" delta="20000" /> 73 <output name="outFileName" file="hicAverageRegions/result_rangeInBins_100.npz" ftype="zip" compare="sim_size" delta="20000" />
71 </test> 74 </test>
72 </tests> 75 </tests>
73 <help><![CDATA[ 76 <help><![CDATA[
74 77
75 Average regions 78 Average regions