Mercurial > repos > bgruening > hicexplorer_chicviewpoint

annotate chicViewpoint.xml @ 8:f881c94fb3b3 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 10:44:35 +0000
parents dbfd2cfc0f66
children
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1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>computes viewpoints with the given reference points and a background model.</description>
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3 <macros>
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4 <token name="@BINARY@">chicViewpoint</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 #import re
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11 #for $m in $matrix_h5_cooler_multiple:
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12 #set identifier = @ESCAPE_IDENTIFIER_M@
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13 ln -s '$m' '$identifier' &&
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14 #end for
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15 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
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17 @BINARY@
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18 --matrices $m
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19 --range $rangeUpstream $rangeDownstream
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20 --referencePoints '$referencePoints'
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21 --averageContactBin $averageContactBin
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22 --fixateRange $fixateRange
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23 --threads @THREADS@
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24 --backgroundModelFile '$backgroundModelFile'
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25 --outFileName interactionFiles.hdf5
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27 ]]> </command>
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28 <inputs>
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29 <expand macro="matrix_h5_cooler_multiple_macro" />
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31 <param argument="--referencePoints" type="data" format="interval" label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." />
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32 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
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33 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
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34
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35 <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
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36 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help="Average the contacts of n bins via a sliding window approach." />
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37 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." />
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38 </inputs>
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39 <outputs>
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40 <data name="interactionFileNames" from_work_dir="interactionFiles.hdf5" format="h5" label="${tool.name} interaction file" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
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45 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
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46 <param name="backgroundModelFile" value="cHi-C/background.txt" />
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47 <param name="fixateRange" value="500000" />
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48 <param name="rangeUpstream" value="200000" />
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49 <param name="rangeDownstream" value="200000" />
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50 <output name="interactionFileNames" ftype="h5">
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51 <assert_contents>
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52 <has_h5_attribute key="averageContactBin" value="5" />
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53 <has_h5_attribute key="fixateRange" value="500000" />
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54 <!-- <has_h5_attribute key="range" value="200000,200000" /> -->
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55 <has_h5_attribute key="resolution" value="1000" />
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56 <has_h5_attribute key="type" value="interactions" />
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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63 Compute viewpoints for all given reference points
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64 =================================================
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66 Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
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67 are named by the name of the reference point, the sample name and the location of the reference point:
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68
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69 gene_matrix_name_chr_start_end.txt
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71 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
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72 file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.
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74 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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76 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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77 ]]> </help>
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78 <expand macro="citations" />
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79 </tool>