Mercurial > repos > bgruening > hicexplorer_hichyperoptdetectloops

annotate hicHyperoptDetectLoops.xml @ 0:dde6b320a34b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
author bgruening
date Tue, 16 Mar 2021 20:14:14 +0000
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children 7f7c6ead2d0d
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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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29
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30 --outputFileName hyperopt_result.txt
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31
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32 --threads @THREADS@
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33 ]]>
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34 </command>
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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35 <inputs>
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36 <expand macro="matrix_h5_cooler_macro" />
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37 <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
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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' />
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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' />
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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' />
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41 </inputs>
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42 <outputs>
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43 <data name='hyperopt_result' from_work_dir='hyperopt_result.txt' format='txt' label='Computed parameters for hicDetectLoops' />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
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48 <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
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49 <param name="maximumNumberOfLoops" value="5" />
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50 <param name="resolution" value="2" />
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51 <param name="runs" value="5" />
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52 <output name="hyperopt_result" file="hicHyperoptDetectLoops/loops.bedgraph" ftype="txt" compare="sim_size" />
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56
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57 Hyperopt parameter optimization loop detection
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58 ==============================================
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59
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60 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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61
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62 _________________
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63
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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64 Usage
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65 -----
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66
dde6b320a34b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
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67 A command line example is available below (easily matchable in Galaxy using each field information):
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68
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69 ̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`
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70
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72 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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73
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74 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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76 ]]> </help>
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77 <expand macro="citations" />
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78 </tool>