Mercurial > repos > bgruening > hicexplorer_hichyperoptdetectloops

annotate 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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dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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1 <tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>optimizes parameters for hicDetectLoops</description>
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3 <macros>
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4 <token name="@BINARY@">hicHyperoptDetectLoops</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
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10 @BINARY@
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11
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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12 --matrix 'matrix.$matrix_h5_cooler.ext'
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dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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14 #if '$proteinFile':
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15 --proteinFile '$proteinFile'
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16 #end if
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18 #if '$maximumNumberOfLoops':
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19 --maximumNumberOfLoops '$maximumNumberOfLoops'
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20 #end if
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dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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22 #if '$resolution':
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23 --resolution '$resolution'
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24 #end if
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26 #if '$runs':
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27 --runs '$runs'
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28 #end if
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7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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30 #if not $prefixLoop_selector == 'keep':
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31 --chrPrefixLoops $prefixLoop_selector
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32 #end if
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33 --outputFileName hyperopt_result.txt
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34
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35 --threads @THREADS@
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36 ]]>
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37 </command>
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38 <inputs>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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39 <expand macro="matrix_h5_cooler_macro" />
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40 <param argument="--proteinFile" type="data" format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
7f7c6ead2d0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
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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" />
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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" />
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43 <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
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44 <option value="keep" selected="True">Keep</option>
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45 <option value="add">Add</option>
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46 <option value="remove">Remove</option>
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47 </param>
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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" />
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49 </inputs>
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50 <outputs>
2
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51 <data name="hyperopt_result" from_work_dir="hyperopt_result.txt" format="txt" label="Computed parameters for hicDetectLoops" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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56 <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
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57 <param name="maximumNumberOfLoops" value="5" />
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58 <param name="resolution" value="2" />
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59 <param name="runs" value="5" />
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60 <output name="hyperopt_result" file="hicHyperoptDetectLoops/loops.bedgraph" ftype="txt" compare="sim_size" />
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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65 Hyperopt parameter optimization loop detection
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66 ==============================================
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67
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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68 Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.
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69
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70 _________________
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71
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72 Usage
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73 -----
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75 A command line example is available below (easily matchable in Galaxy using each field information):
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76
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77 ̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`
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80 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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81
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82 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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84 ]]> </help>
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85 <expand macro="citations" />
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86 </tool>