Mercurial > repos > bgruening > hicexplorer_hicaggregatecontacts

annotate hicAggregateContacts.xml @ 0:ccd1d3013827 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:37:18 -0500
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children ec59bf4c3d06
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ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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1 <tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Takes a list of positions in the hic-matrix and makes a pooled image</description>
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3 <macros>
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4 <token name="@BINARY@">hicAggregateContacts</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 @BINARY@
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10 --matrix '$matrix_h5_cooler'
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11 --BED $BED
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12 #if $BED2:
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13 --BED2 $BED2
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14 #end if
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15
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16 --range $range_min:$range_max
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17
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18 --numberOfBins $numberOfBins
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20 --transform $transform
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21 --avgType $avgType
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22
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23 #if $outputs and 'PrefixMatrix' in $outputs:
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24 --outFilePrefixMatrix 'matrix_values'
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25 #end if
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26
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27 #if $outputs and 'ClusterContactPositions' in $outputs:
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28 --outFilePrefixClusterContactPositions 'contact_positions'
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29 #end if
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30
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31 #if $outputs and 'HeatmapFile' in $outputs:
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32 --diagnosticHeatmapFile 'heatmap'
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33 #end if
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34
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35 #if $clustering:
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36 $clustering
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37 #end if
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38 $clusterOnDiagonal
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39
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40 #if $chromosomes:
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41 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
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42 #end if
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43
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44 #if $plotType:
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45 --plotType $plotType
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46 #end if
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47
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48 #if $colormap:
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49 --colorMap $colormap
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50 #end if
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51
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52 #if $vMin:
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53 --vMin $vMin
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54 #end if
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55
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56 #if $vMax:
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57 --vMax $vMax
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58 #end if
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59
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60 --outFileName plot.$image_file_format
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61 && mv plot.$image_file_format plot
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62
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63 ]]>
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64 </command>
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65 <inputs>
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66 <expand macro='matrix_h5_cooler_macro' />
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67 <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted."/>
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68 <param argument="--BED2" type="data" format="bed" optional="true"
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69 label="Interactions between regions in first and second BED file are plotted."/>
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70
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71 <expand macro='range' />
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72
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73 <repeat name="chromosomes" title="List of chromosomes to plot" min="0">
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74 <param name="chromosome" type="text">
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75 <validator type="empty_field" />
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76 </param>
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77 </repeat>
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78
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79 <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix"
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80 help=" The bed regions will be centered between - half number of bins
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81 and the other half number of bins." />
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82
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83 <param argument="--transform" type="select" label="Type of transformation for the matrix"
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84 help="If total counts are selected, then the sub-matrix values
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85 are divided by the total counts for normalization. If
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86 z-score or obs/exp are selected, then H-C matrix is
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87 converted into a z-score or observed / expected matrix.">
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88 <option value="none" selected="true">none</option>
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89 <option value="total-counts">total-counts</option>
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90 <option value="z-score">z-score</option>
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91 <option value="obs/exp">obs/exp</option>
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92 </param>
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93
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94 <param argument="--avgType" type="select" label="Type of average to compute final matrix">
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95 <option value="median" selected="true">median</option>
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96 <option value="mean">mean</option>
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97 </param>
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98
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99 <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome"
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100 help="When this option is set, then the matrix is split into
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101 clusters using the hierarchical clustering algorithm,
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102 using 'ward linkage'. --hclust could be very slow if
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103 you have >1000 submatrices per chromosome. In those
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104 cases, you might prefer --kmeans">
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105 <option value="--kmeans">kmenas</option>
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106 <option value="--hclust">hclust (#clusters per chromosome)</option>
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107 </param>
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108
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109 <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue=""
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110 label="Perform clustering on the submatrix diagonal"
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111 help="Clustering is by default carried out on the whole
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112 submatrices. If this parameter is given, the
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113 clustering is only carried out based on the submatrix
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114 diagonal (representing values at the same distance to each other)" />
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115
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116 <param argument="--plotType" type="select" optional="true" label="Plot type">
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117 <option value="2d">2D</option>
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118 <option value="3d">3D</option>
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119 </param>
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120 <expand macro="colormap" />
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121 <param argument="--vMin" type="float" optional="true" label="vMin"/>
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122 <param argument="--vMax" type="float" optional="true" label="vMax"/>
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123
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124 <param name="image_file_format" type="select" label="Image output format">
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125 <option value="png" selected="True">png</option>
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126 <option value="svg">svg</option>
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127 </param>
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128
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129 <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
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130 <option value="PrefixMatrix">Save values underlying the final matrix</option>
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131 <option value="ClusterContactPositions">Save the position of the contacts</option>
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132 <option value="HeatmapFile">Heatmap file per chromosome</option>
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133 </param>
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134
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135 </inputs>
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136 <outputs>
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137 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}">
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138 <change_format>
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139 <when input="image_file_format" value="svg" format="svg" />
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140 </change_format>
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141 </data>
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142 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
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143 <discover_datasets pattern="matrix_values_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
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144 </collection>
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145 <collection name="contact_positions" type="list" label="${tool.name} on ${on_string}: Matrix values">
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146 <discover_datasets pattern="contact_positions_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
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147 </collection>
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148 <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Matrix values">
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149 <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
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150 </collection>
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151 </outputs>
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152 <tests>
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153 <test>
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154 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/>
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155 <param name="BED" value="test_regions.bed" ftype="bed"/>
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156 <param name="numberOfBins" value="30" />
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157 <param name="range_max" value="900000" />
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158 <param name="range_min" value="50000" />
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159 <param name="image_file_format" value="png" />
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160 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
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161 </test>
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162 </tests>
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163 <help><![CDATA[
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164 --outFilePrefixMatrix OUTFILEPREFIXMATRIX
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165 If this option is given, then the values underlying
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166 the final matrix will be saved to tab-delimited tables
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167 (one per chromosome) using the indicated prefix, for
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168 example TSS_to_TSS_chrX.tab. If clustering is
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169 performed, then the values are saved including the
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170 cluster_id a in TSS_to_TSS_chrX_cluster_1.tab
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171 --outFilePrefixClusterContactPositions OUTFILEPREFIXCLUSTERCONTACTPOSITIONS
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172 If this option is given, then the position of the
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173 contacts is saved as (chrom1, start1, end1, chrom2,
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174 start2, end2) where chrom_n, start_n, end_n correspond
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175 to the pair ofpositions used to compute the submatrix.
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176 The data is saved per chromosome and per cluster
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177 separatedly (one file each)
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178 --diagnosticHeatmapFile DIAGNOSTICHEATMAPFILE
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179 If given, a heatmap file (per chromosome) is saved.
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180 Each row in the heatmap contains thediagonal of each
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181 of the submatrices centered on the bed file. This file
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182 is useful to get an idea of the values that are used
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183 for the aggregate matrix and to determine the fraction
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184 of sub-matrices that are aggregated that may have an
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185 enrichment at the center.
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186
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187
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188
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189 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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190
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191 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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192 ]]></help>
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193 <expand macro="citations" />
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194 </tool>