Mercurial > repos > iuc > schicexplorer_schicplotconsensusmatrices

annotate scHicPlotConsensusMatrices.xml @ 3:b1f0a9b02efd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
author iuc
date Thu, 31 Jul 2025 16:45:18 +0000
parents 95b1216e1e70
children
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95b1216e1e70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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1 <tool id="schicexplorer_schicplotconsensusmatrices" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
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2 <description>plot single-cell Hi-C interaction matrices cluster consensus matrices</description>
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3 <macros>
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4 <token name="@BINARY@">scHicPlotConsensusMatrices</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements" />
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9 <command detect_errors="exit_code"><![CDATA[
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10 @BINARY@
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11
1
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12 --matrix $matrix_scooler
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13 #if $chromosomes:
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14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
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15 --chromosomes $chromosome
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16 #end if
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17
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18 #if $colormap:
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19 --colorMap $colormap
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20 #end if
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21 #if $dpi:
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22 --dpi $dpi
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23 #end if
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24 --outFileName plot.$image_file_format
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25
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26 --threads @THREADS@
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28 && mv plot.$image_file_format plot
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29
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30 ]]></command>
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31 <inputs>
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32 <expand macro="matrix_scooler_macro"/>
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33 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
1a1e085c352e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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34 <expand macro="colormap" />
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35 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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36
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37 <param name="image_file_format" type="select" label="Image output format">
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38 <option value="png" selected="True">png</option>
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39 <option value="svg">svg</option>
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40 <option value="pdf">pdf</option>
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41 </param>
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42
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43 </inputs>
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44 <outputs>
1
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45 <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'>
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46 <change_format>
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47 <when input="image_file_format" value="svg" format="svg" />
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48 <when input="image_file_format" value="pdf" format="pdf" />
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49 </change_format>
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50 </data>
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51 </outputs>
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52 <tests>
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53 <test>
1
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54 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
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55 <param name="image_file_format" value="png" />
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56 <param name="dpi" value="300" />
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57 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>
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58 </test>
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59 <test>
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60 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
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61 <param name="image_file_format" value="png" />
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62 <param name="dpi" value="300" />
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63 <param name="chromosomes" value="chr1 chr2" />
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64
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65 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>
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66 </test>
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67
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68 </tests>
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69 <help><![CDATA[
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70
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71 Plot consensus matrices
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72 =======================
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73
1
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74 scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. This tool is useful to compare the single cell clusters.
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75
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76 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png
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77 :width: 50%
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78
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79 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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80
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81 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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82 ]]></help>
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83 <expand macro="citations" />
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84
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b1f0a9b02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
iuc
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85 </tool>