Mercurial > repos > bgruening > hicexplorer_hichyperoptdetectloops

comparison hicHyperoptDetectLoops.xml @ 2:7f7c6ead2d0d 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 10:36:42 +0000
parents dde6b320a34b
children 409396ea5cf0
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equal deleted inserted replaced
1:89fb1aab755b 2:7f7c6ead2d0d
24 #end if 24 #end if
25 25
26 #if '$runs': 26 #if '$runs':
27 --runs '$runs' 27 --runs '$runs'
28 #end if 28 #end if
29 29
30 #if not $prefixLoop_selector == 'keep':
31 --chrPrefixLoops $prefixLoop_selector
32 #end if
30 --outputFileName hyperopt_result.txt 33 --outputFileName hyperopt_result.txt
31 34
32 --threads @THREADS@ 35 --threads @THREADS@
33 ]]> 36 ]]>
34 </command> 37 </command>
35 <inputs> 38 <inputs>
36 <expand macro="matrix_h5_cooler_macro" /> 39 <expand macro="matrix_h5_cooler_macro" />
37 <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." /> 40 <param argument="--proteinFile" type="data" format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
38 <param argument="--maximumNumberOfLoops" type="integer" min='0' max='100000' label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value='10000' /> 41 <param argument="--maximumNumberOfLoops" type="integer" min="0" max="100000" label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value="10000" />
39 <param argument="--resolution" type="integer" min='0' max='100000000' label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value='10000' /> 42 <param argument="--resolution" type="integer" min="0" max="100000000" label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value="10000" />
40 <param argument="--runs" type="integer" min='2' max='10000' label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value='100' /> 43 <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
44 <option value="keep" selected="True">Keep</option>
45 <option value="add">Add</option>
46 <option value="remove">Remove</option>
47 </param>
48 <param argument="--runs" type="integer" min="2" max="10000" label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value="100" />
41 </inputs> 49 </inputs>
42 <outputs> 50 <outputs>
43 <data name='hyperopt_result' from_work_dir='hyperopt_result.txt' format='txt' label='Computed parameters for hicDetectLoops' /> 51 <data name="hyperopt_result" from_work_dir="hyperopt_result.txt" format="txt" label="Computed parameters for hicDetectLoops" />
44 </outputs> 52 </outputs>
45 <tests> 53 <tests>
46 <test> 54 <test>
47 <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> 55 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
48 <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" /> 56 <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />