Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

annotate hicPlotDistVsCounts.xml @ 5:819bd2c44d4a draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:29:00 -0500
parents ed96f2fd7e3f
children 62803bb47880
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1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>distance vs HiC counts plot per chromosome</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotDistVsCounts</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="aggressive"><![CDATA[
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9 #import re
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10 #set matrices_path=[]
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11 #set matrices_labels=[]
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12 #for $counter, $m, in enumerate($matrices):
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13 #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier))
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14 ln -f -s '${m}' '${identifier}_${counter}' &&
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15 #silent $matrices_path.append("'%s_%s'" % ($identifier, $counter))
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16 #silent $matrices_labels.append("'%s'" % ($identifier))
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17 #end for
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18
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19 @BINARY@
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20 --matrices #echo " ".join($matrices_path)#
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21 --labels #echo " ".join($matrices_labels)#
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22 $skipDiagonal
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23 --plotFile plot.png
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24 #if $plotsize:
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25 --plotsize $plotsize
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26 #end if
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27 --maxdepth $maxdepth
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28 $perchr
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29 #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ])
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30 #if $chromosomeExclude:
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31 --chromosomeExclude '$chroms'
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32 #end if
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="HiC normalized (corrected) matrices"/>
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37
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38 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
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39 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
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40 help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
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41 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
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42 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
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43 <param argument="--plotsize" type="text" optional="True" label="Plot size"
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44 help="Width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example --plotsize 6 5." />
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45 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
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46 help="This is useful for example to exclude the Y chromosome.">
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47 <param argument="--chromosomeExclude" type="text" value="" >
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48 <validator type="empty_field" />
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49 </param>
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50 </repeat>
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51
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52 </inputs>
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53 <outputs>
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54 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
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59 <param name="skipDiagonal" value="False"/>
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60 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
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61 </test>
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62 <test>
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63 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
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64 <param name="skipDiagonal" value="False"/>
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65 <param name="perchr" value="True" />
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66 <repeat name="chromosomeExclude">
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67 <param name="chromosomeExclude" value="chrUextra"/>
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68 </repeat>
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69 <repeat name="chromosomeExclude">
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70 <param name="chromosomeExclude" value="chrM"/>
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71 </repeat>
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72 <repeat name="chromosomeExclude">
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73 <param name="chromosomeExclude" value="chr3LHet"/>
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74 </repeat>
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75 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 Relation of genomic distance and number of contacts
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80 ========================================================
0
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81
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82 | This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
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83 | them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case
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84 | of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
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85 | matrices denser matrices are scaled down to match the sum of the smaller matrix.
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86 |
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87 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
0
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88
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89
4
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90 Input
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91 -----
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92
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93 Parameters
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94 __________
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95 - contact matrix
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96 - skip diagonal
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97 - per chromosome
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98 - max depth
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99 - plot size
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100 - chromosome(s) to exclude
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101
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102 Output
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103 -------
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104 Output if all data in the contact matrix is considered:
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105
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106 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png
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107 :width: 70%
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108
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109 Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome:
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110
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111 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
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112 :width: 80%
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113
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114 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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115 ]]></help>
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116 <expand macro="citations" />
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117 </tool>
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118