Mercurial > repos > bgruening > deeptools_compute_matrix

annotate computeMatrix.xml @ 5:345a9a2281e0 draft

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author bgruening
date Tue, 22 Dec 2015 13:47:40 -0500
parents 2f2dd609644f
children 451e73bf38fe
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1 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
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2 <description>prepares data for plotting a heatmap or a profile of given regions</description>
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3 <macros>
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4 <token name="@BINARY@">computeMatrix</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 #import tempfile
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11
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12 @BINARY@
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13
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14 $mode.mode_select
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15 --regionsFileName
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16 #for $rf in $regionsFiles:
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17 '$rf.regionsFile'
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18 #end for
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19 --scoreFileName
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20 #for $bw in $scoreFileName:
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21 '$bw'
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22 #end for
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23 --outFileName '$outFileName'
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25 @THREADS@
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26
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27 #if $output.showOutputSettings == "yes"
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28 #if $output.saveMatrix:
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29 --outFileNameMatrix '$outFileNameMatrix'
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30 #end if
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31
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32 #if $output.saveSortedRegions:
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33 --outFileSortedRegions '$outFileSortedRegions'
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34 #end if
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35 #end if
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36
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37 #if $mode.mode_select == "reference-point":
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38 --referencePoint $mode.referencePoint
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39 $mode.nanAfterEnd
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40 --beforeRegionStartLength $mode.beforeRegionStartLength
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41 --afterRegionStartLength $mode.afterRegionStartLength
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42 #else
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43 --regionBodyLength $mode.regionBodyLength
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44 --startLabel "$mode.startLabel"
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45 --endLabel "$mode.endLabel"
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46 #if $mode.regionStartLength.regionStartLength_select == "yes":
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47 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
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48 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
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49 #end if
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50 #end if
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51
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52 #if $advancedOpt.showAdvancedOpt == "yes":
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53 --sortRegions '$advancedOpt.sortRegions'
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54 --sortUsing '$advancedOpt.sortUsing'
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55 --averageTypeBins '$advancedOpt.averageTypeBins'
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56 $advancedOpt.skipNAs
0
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57 $advancedOpt.skipZeros
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58 --binSize $advancedOpt.binSize
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59
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60 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
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61 --minThreshold $advancedOpt.minThreshold
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62 #end if
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63 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
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64 --maxThreshold $advancedOpt.maxThreshold
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65 #end if
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66 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
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67 --scale $advancedOpt.scale
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68 #end if
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69
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70 #end if
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71 ]]>
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72 </command>
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73 <inputs>
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74
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75 <repeat name="regionsFiles" title="regions to plot" min="1">
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76 <param name="regionsFile" format="bed" type="data" label="Regions to plot"
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77 help="File, in BED format, containing the regions to plot."/>
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78 <param name="label" type="text" size="30" optional="true" value="" label="Label"
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79 help="Label to use in the output."/>
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80 </repeat>
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81
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82 <param name="scoreFileName" format="bigwig" type="data"
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83 label="Score file" multiple="True"
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84 help="Should be a bigWig file (containing a score, usually covering
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85 the whole genome). You can generate a bigWig file either from a
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86 bedGraph or WIG file using UCSC tools or from a BAM file using the
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87 deepTool bamCoverage. (--scoreFileName)"/>
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88
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89 <conditional name="mode" >
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90 <param name="mode_select" type="select"
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91 label="computeMatrix has two main output options"
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92 help="In the scale-regions mode, all regions in the BED file are
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93 stretched or shrunk to the same length (bp) that is indicated
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94 by the user. Reference-point refers to a position within the BED
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95 regions (e.g start of region). In the reference-point mode only
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96 those genomic positions before (downstream) and/or after (upstream)
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97 the reference point will be plotted.">
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98 <option value="scale-regions" selected="true">scale-regions</option>
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99 <option value="reference-point">reference-point</option>
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100 </param>
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101
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102 <when value="scale-regions" >
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103 <param argument="--regionBodyLength" type="integer" value="500"
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104 label="Distance in bp to which all regions are going to be fitted" help=""/>
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105 <param argument="--startLabel" type="text" value="TSS" size="10"
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106 label="Label for the region start"
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107 help ="Label shown in the plot for the start of the region.
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108 Default is TSS (transcription start site), but could be changed to anything,
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109 e.g. &quot;peak start&quot;." />
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110 <param argument="--endLabel" type="text" value="TES" size="10"
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111 label="Label for the region end"
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112 help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
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113 <conditional name="regionStartLength">
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114 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
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115 <option value="no" selected="true">no</option>
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116 <option value="yes">yes</option>
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117 </param>
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118 <when value="no" />
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119 <when value="yes">
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120 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
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121 label="Distance upstream of the start site of the regions defined in the region file"
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122 help="If the regions are genes, this would be the
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123 distance upstream of the transcription start site."/>
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124 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
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125 label="Distance downstream of the end site of the given regions"
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126 help="If the regions are genes, this would be the
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127 distance downstream of the transcription end site."/>
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128 </when>
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129 </conditional>
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130 </when>
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131 <when value="reference-point">
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132 <param name="referencePoint" type="select" label="The reference point for the plotting">
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133 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
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134 <option value="TES">end of region (e.g. TES)</option>
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135 <option value="center">center of region</option>
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136 </param>
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137 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue=""
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138 label="Discard any values after the region end"
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139 help="This is useful to visualize the region end when not using the
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140 scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/>
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141 <param name="beforeRegionStartLength" type="integer" value="1000" min="1"
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142 label="Distance upstream of the start site of the regions defined in the region file"
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143 help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/>
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144 <param name="afterRegionStartLength" type="integer" value="1000" min="1"
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145 label="Distance downstream of the end site of the given regions"
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146 help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/>
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147 </when>
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148 </conditional>
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149
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150 <expand macro="input_graphic_output_settings">
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151 <expand macro="input_save_matrix_values" />
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152 </expand>
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153
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154 <conditional name="advancedOpt" >
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155 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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156 <option value="no" selected="true">no</option>
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157 <option value="yes">yes</option>
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158 </param>
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159 <when value="no" />
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160 <when value="yes">
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161 <param name="binSize" type="integer" value="50" min="1"
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162 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length"
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163 help="(--binSize)"/>
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164
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165 <expand macro="sortRegions" />
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166 <expand macro="sortUsing" />
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167
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168 <param name="averageTypeBins" type="select"
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169 label="Define the type of statistic that should be displayed."
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170 help="The value is computed for each bin. (--averageTypeBins)">
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171 <option value="mean" selected="true">mean</option>
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172 <option value="median">median</option>
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173 <option value="min">min</option>
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174 <option value="max">max</option>
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175 <option value="sum">sum</option>
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176 <option value="std">std</option>
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177 </param>
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178
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179 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
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180 label="Convert missing values to 0?."
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181 help="If set to 'yes', missing values (NAs) are converted to 0.
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182 The default is to ignore such cases, which will be
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183 depicted as black areas in the heatmap by default." />
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184
0
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185 <expand macro="skipZeros" />
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186 <expand macro="skipNAs" />
0
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187
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188 <param name="minThreshold" type="float" optional="True"
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189 label="Minimum threshold"
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190 help="Any region containing a value that is equal or less than this numeric
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191 value will be skipped. This is useful to skip, for example, genes where the
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192 read count is zero for any of the bins. This could be the result of
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193 unmappable areas and can bias the overall results. (--minThreshold)"/>
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194 <param name="maxThreshold" type="float" optional="True"
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195 label="Maximum threshold"
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196 help="Any region containing a value that is equal or higher that this
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197 numeric value will be skipped. The max threshold is useful to skip those
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198 few regions with very high read counts (e.g. major satellites) that may
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199 bias the average values. (--maxThreshold)"/>
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200 <param name="scale" type="float" optional="True" label="Scaling factor"
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201 help="If set, all values are multiplied by this number. (--scale)"/>
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202 </when>
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203 </conditional>
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204 </inputs>
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205 <outputs>
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206 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
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207 <expand macro="output_graphic_outputs" />
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208 <expand macro="output_save_matrix_values" />
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209 </outputs>
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210 <!--
5
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211 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
0
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212 -->
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213 <tests>
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214 <test>
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215 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
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216 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
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217 <param name="showAdvancedOpt" value="yes" />
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218 <param name="mode_select" value="reference-point" />
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219 <param name="binSize" value="10" />
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220 <param name="sortUsing" value="sum" />
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221 <param name="averageTypeBins" value="sum" />
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222 <param name="skipNAs" value="False" />
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223 <param name="beforeRegionStartLength" value="10" />
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224 <param name="afterRegionStartLength" value="10" />
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225 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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226 </test>
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227 <test>
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228 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
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229 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
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230 <param name="showAdvancedOpt" value="yes" />
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231 <param name="mode_select" value="reference-point" />
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232 <param name="binSize" value="10" />
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233 <param name="beforeRegionStartLength" value="10" />
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234 <param name="afterRegionStartLength" value="10" />
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235 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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236 </test>
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237 <test>
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238 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
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239 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
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240 <param name="showAdvancedOpt" value="yes" />
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241 <param name="mode_select" value="scale-regions" />
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242 <param name="endLabel" value="END" />
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243 <param name="regionStartLength" value="yes" />
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244 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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245 </test>
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246 </tests>
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247 <help>
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248 <![CDATA[
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249 **What it does**
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250
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251 This tool prepares an intermediary file (a gzipped table of values)
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252 that contains scores associated with genomic regions that can be used
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253 afterwards to plot a heatmap or a profile.
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254
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255 Genomic regions can really be anything - genes, parts of genes, ChIP-seq
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256 peaks, favorite genome regions... as long as you provide a proper file
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257 in BED or INTERVAL format. If you would like to compare different groups of regions
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258 (i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.
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259
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260 computeMatrix can also be used to filter and sort
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261 regions according to their score by making use of its advanced output options.
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262
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264 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
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265 :alt: Relationship between computeMatrix, heatmapper and profiler
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268 You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html
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271 -----
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273 @REFERENCES@
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274 ]]>
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275 </help>
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276 <expand macro="citations" />
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277 </tool>