Mercurial > repos > iuc > schicexplorer_schicplotclusterprofiles

annotate scHicPlotClusterProfiles.xml @ 1:9da580a74230 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:12:42 -0400
parents 2427c6d8cdd0
children 65f2f5d29947
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2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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1 <tool id="schicexplorer_schicplotclusterprofiles" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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2 <description>plot single-cell Hi-C interaction matrices cluster profiles</description>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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3 <macros>
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4 <token name="@BINARY@">scHicPlotClusterProfiles</token>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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5 <import>macros.xml</import>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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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[
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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9 @BINARY@
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10
1
9da580a74230 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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11 --matrix $matrix_scooler
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2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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12 --clusters $clusters
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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13 #if $chromosomes:
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14 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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15 --chromosomes $chromosome
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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16 #end if
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17
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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18 #if $order_by_conditional.order_by_selection == 'orderByFile':
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19 --orderBy $order_by_conditional.order_by_selection
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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20 #elif $order_by_conditional.order_by_selection == 'svl':
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21 --orderBy $order_by_conditional.order_by_selection
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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22 --distanceShortRange $order_by_conditional.distanceShortRange
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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23 --distanceLongRange $order_by_conditional.distanceLongRange
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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24 #end if
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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25 #if $dpi:
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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26 --dpi $dpi
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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27 #end if
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28 --outFileName plot.$image_file_format
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29
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30 --threads @THREADS@
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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31
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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32 && mv plot.$image_file_format plot
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33
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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34 ]]></command>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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35 <inputs>
1
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36 <expand macro="matrix_scooler_macro"/>
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37 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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38 <param name="maximalDistance" type="integer" value="2000000" label="Maximal distance" help='Maximal distance to consider for plotting' />
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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39 <conditional name="order_by_conditional">
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40 <param name='order_by_selection' label='Order samples by' type='select'>
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41 <option value='svl' selected='true'>Short vs long range ratio</option>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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42 <option value='orderByFile'>Order by file</option>
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43 </param>
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44 <when value='svl' >
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45 <param name="distanceShortRange" type="integer" value="2000000" label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />
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46 <param name="distanceLongRange" type="integer" value="12000000" label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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47 </when>
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48 <when value='orderByFile'>
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49 </when>
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50 </conditional>
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51 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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52 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
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53
2427c6d8cdd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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54 <param name="image_file_format" type="select" label="Image output format">
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55 <option value="png" selected="True">png</option>
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56 <option value="svg">svg</option>
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57 <option value="pdf">pdf</option>
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58 </param>
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59
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60 </inputs>
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61 <outputs>
1
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62 <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '>
0
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63 <change_format>
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64 <when input="image_file_format" value="svg" format="svg" />
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65 <when input="image_file_format" value="pdf" format="pdf" />
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66 </change_format>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <test>
1
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71 <param name='matrix_scooler' value='test_matrix.scool' />
0
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72 <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' />
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73 <conditional name="order_by_conditional">
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74 <param name="order_by_selection" value="svl"/>
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75 <param name="distanceShortRange" value="2000000" />
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76 <param name="distanceLongRange" value="12000000" />
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77 </conditional>
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78 <param name="maximalDistance" value="50000000" />
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79 <param name="image_file_format" value="png" />
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80 <param name="dpi" value="300" />
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81
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82 <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/>
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83 </test>
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84
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85 </tests>
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86 <help><![CDATA[
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87
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88 Plot cluster profiles
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89 =====================
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90
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91 scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix associated to a cluster, within the cluster the matrices can be ordered either via their short vs long range ratio or by the order of the file.
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92 This tool is useful as a quality control of a cluster to check if all matrices assigned to that cluster are displaying similar contacts distribution.
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93
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94 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png
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95 :width: 50%
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96
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97 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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98
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99 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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100 ]]></help>
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101 <expand macro="citations" />
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102
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103 </tool>