Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix

comparison hicAdjustMatrix.xml @ 8:2dccb6bb0add draft default tip

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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 10:42:59 +0000
parents a7fd644deda6
children
comparison
equal deleted inserted replaced
7:aeacaf08bd52 8:2dccb6bb0add
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 #if not $interIntra_selector == 'keep':
29 --interIntraHandling $interIntra_selector
30 #end if
28 && mv '$matrix_file_out' matrix 31 && mv '$matrix_file_out' matrix
32
29 ]]> 33 ]]>
30 </command> 34 </command>
31 <inputs> 35 <inputs>
32 <expand macro='matrix_h5_cooler_macro' /> 36 <expand macro="matrix_h5_cooler_macro" />
33 <param name="action_selector" type="select" label="Apply action"> 37 <param name="action_selector" type="select" label="Apply action">
34 <option value="keep" selected="True">keep</option> 38 <option value="keep" selected="True">keep</option>
35 <option value="remove">remove</option> 39 <option value="remove">remove</option>
36 <option value="mask">mask</option> 40 <option value="mask">mask</option>
37 </param> 41 </param>
49 </when> 53 </when>
50 <when value="optionRegionFile"> 54 <when value="optionRegionFile">
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." /> 55 <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." />
52 </when> 56 </when>
53 </conditional> 57 </conditional>
58 <param name="interIntra_selector" type="select" label="Remove inter- or intra chromosomal regions">
59 <option value="keep" selected="True">Do not apply</option>
60 <option value="inter">Remove inter-chromosomal contacts</option>
61 <option value="intra">Remove intra-chromosomal contacts</option>
62 </param>
54 </inputs> 63 </inputs>
55 <outputs> 64 <outputs>
56 <data name="outFileName" from_work_dir="matrix" format="h5"> 65 <data name="outFileName" from_work_dir="matrix" format="h5">
57 <change_format> 66 <change_format>
58 <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> 67 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
62 <tests> 71 <tests>
63 <test expect_num_outputs="1"> 72 <test expect_num_outputs="1">
64 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> 73 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
65 <param name="action_selector" value="keep" /> 74 <param name="action_selector" value="keep" />
66 <conditional name="chromosomeOrRegionFile_conditional"> 75 <conditional name="chromosomeOrRegionFile_conditional">
67 <param name="chromosomeOrRegionFile_selector" value='optionChromosomes' /> 76 <param name="chromosomeOrRegionFile_selector" value="optionChromosomes" />
68 <repeat name="chromosomeOrder"> 77 <repeat name="chromosomeOrder">
69 <param name="chromosome" value='chrX' /> 78 <param name="chromosome" value="chrX" />
70 <param name="chromosome" value='chr3R' /> 79 <param name="chromosome" value="chr3R" />
71 </repeat> 80 </repeat>
72 </conditional> 81 </conditional>
73 <output name="outFileName" ftype="h5"> 82 <output name="outFileName" ftype="h5">
74 <assert_contents> 83 <assert_contents>
75 <has_h5_keys keys='intervals,matrix' /> 84 <has_h5_keys keys="intervals,matrix" />
76 </assert_contents> 85 </assert_contents>
77 </output> 86 </output>
78 </test> 87 </test>
79 <test expect_num_outputs="1"> 88 <test expect_num_outputs="1">
80 <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> 89 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
81 <param name="action_selector" value="mask" /> 90 <param name="action_selector" value="mask" />
82 <conditional name="chromosomeOrRegionFile_conditional"> 91 <conditional name="chromosomeOrRegionFile_conditional">
83 <param name="chromosomeOrRegionFile_selector" value='optionRegionFile' /> 92 <param name="chromosomeOrRegionFile_selector" value="optionRegionFile" />
84 <param name="regions" value='regions.bed' /> 93 <param name="regions" value="regions.bed" />
85 </conditional> 94 </conditional>
86 <output name="outFileName" ftype="h5"> 95 <output name="outFileName" ftype="h5">
87 <assert_contents> 96 <assert_contents>
88 <has_h5_keys keys='intervals,matrix,nan_bins' /> 97 <has_h5_keys keys="intervals,matrix,nan_bins" />
89 </assert_contents> 98 </assert_contents>
90 </output> 99 </output>
91 </test> 100 </test>
92 </tests> 101 </tests>
93 <help><![CDATA[ 102 <help><![CDATA[