Mercurial > repos > bgruening > hicexplorer_hiccorrelate

annotate hicCorrelate.xml @ 4:c153ea23aca8 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:34:28 -0500
parents ae2d7e2dfeef
children c1f9dc3b2238
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fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Computes pairwise correlations between hic matrices data</description>
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3 <macros>
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4 <token name="@BINARY@">hicCorrelate</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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10 @multiple_input_matrices@
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11 hicCorrelate
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13 --matrices $matrices
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14 --labels $mlabels
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16 #if $method and $method is not None:
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17 --method $method
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18 #end if
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19 $log1p
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21 #if $use_range.select_use_range == "yes_use_range":
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22 --range $range_min:$range_max
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23 #end if
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25 #if $chromosomes:
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26 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
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27 #end if
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28
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29 --colorMap $colormap
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31 --outFileNameHeatmap ./heatmap.png
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32 --outFileNameScatter ./scatter.png
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33 ]]>
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34 </command>
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35 <inputs>
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36 <expand macro="multiple_input_matrices" />
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37
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38 <param name="method" type="select" label="Correlation method to use" argument="--method" >
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39 <option value="spearman">Spearman</option>
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40 <option selected="true" value="pearson">Pearson</option>
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41 </param>
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42 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue=""
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43 label="Use the log1p of the matrix values" help="(--log1p)" />
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44 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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45 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
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46 <option value="no_use_range">No restriction</option>
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47 <option value="yes_use_range">Only consider counts within a range</option>
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48 </param>
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49 <when value="no_use_range"/>
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50 <when value="yes_use_range">
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51 <param name="range_min" type="integer" value="" min="0"/>
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52 <param name="range_max" type="integer" value="" min="0"/>
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53 </when>
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54 </conditional>
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55 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
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56 <param name="chromosome" type="text">
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57 <validator type="empty_field" />
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58 </param>
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59 </repeat>
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61 <expand macro="colormap" />
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62
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63 </inputs>
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64 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
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65 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
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66 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
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67 </outputs>
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68 <tests>
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69 <test>
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70 <repeat name="input_files">
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71 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
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72 <param name="mlabel" value="first"/>
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73 </repeat>
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74 <repeat name="input_files">
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75 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
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76 <param name="mlabel" value="second"/>
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77 </repeat>
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78 <param name="log1p" value="True"/>
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79 <param name="colormap" value="jet"/>
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80 <param name="method" value="spearman"/>
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81 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
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82 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
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83 </test>
2
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84 <test>
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85 <repeat name="input_files">
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86 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
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87 <param name="mlabel" value="first"/>
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88 </repeat>
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89 <repeat name="input_files">
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90 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
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91 <param name="mlabel" value="second"/>
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92 </repeat>
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93
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94 <param name="log1p" value="True"/>
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95 <param name="colormap" value="jet"/>
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96 <param name="method" value="spearman"/>
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97 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
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98 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
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99 </test>
0
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100 </tests>
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101 <help><![CDATA[
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102
4
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103 Matrix correlation
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104 ==================
0
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105
4
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106 Computes pairwise correlations between Hi-C contact matrices.
0
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107 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
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108
4
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109 Input
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110 -----
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111
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112 Parameters
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113 __________
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114 - Two contact matrices which are used for the correlation.
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115 - Choice if pearson or spearman correlation should be used.
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116 - log scale for the values
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117 - Correlate full matrix or only specific chromosomes
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118 - Correlate only within a given range.
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119 - colormap to use: Colormap_
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120
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121 Output
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122 ------
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123
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124 Pearson correlation
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125 ___________________
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126
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127 |pearson| |pearson_scatter|
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128
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129 .. |pearson| image:: $PATH_TO_IMAGES/hicCorrelate_pearson.png
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130 :width: 45%
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131
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132 .. |pearson_scatter| image:: $PATH_TO_IMAGES/hicCorrelate_pearson_scatter.png
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133 :width: 45%
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134
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135 Scatter plot
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136
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137 Spearman correlation
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138 _____________________
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139
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140 |spearman| |spearman_scatter|
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141
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142 .. |spearman| image:: $PATH_TO_IMAGES/hicCorrelate_spearman.png
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143 :width: 45 %
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144
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145 .. |spearman_scatter| image:: $PATH_TO_IMAGES/hicCorrelate_spearman_scatter.png
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146 :width: 45 %
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147
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148 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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149
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150 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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151 .. _Colormap: https://matplotlib.org/examples/color/colormaps_reference.html
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152
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153 ]]></help>
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154 <expand macro="citations" />
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155 </tool>