Mercurial > repos > bgruening > deeptools_compute_matrix

annotate computeMatrix.xml @ 0:14cb57237e46 draft

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author bgruening
date Mon, 25 Jan 2016 20:26:32 -0500
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children 275ed3e83de0
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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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24
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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 #if $mode.regionStartLength.regionStartLength_select == "yes":
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45 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
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46 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
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47 #end if
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48 #end if
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49
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50 #if $advancedOpt.showAdvancedOpt == "yes":
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51 --sortRegions '$advancedOpt.sortRegions'
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52 --sortUsing '$advancedOpt.sortUsing'
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53 --averageTypeBins '$advancedOpt.averageTypeBins'
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54 $advancedOpt.skipNAs
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55 $advancedOpt.skipZeros
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56 --binSize $advancedOpt.binSize
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57
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58 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
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59 --minThreshold $advancedOpt.minThreshold
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60 #end if
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61 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
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62 --maxThreshold $advancedOpt.maxThreshold
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63 #end if
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64 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
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65 --scale $advancedOpt.scale
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66 #end if
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67
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68 #end if
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69 ]]>
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70 </command>
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71 <inputs>
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72
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73 <repeat name="regionsFiles" title="Select regions" min="1">
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74 <param name="regionsFile" format="bed" type="data" label="Regions to plot"
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75 help="File, in BED format, containing the regions to plot."/>
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76 </repeat>
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77
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78 <param name="scoreFileName" format="bigwig" type="data"
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79 label="Score file" multiple="True"
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80 help="You can generate a bigWig file from either a
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81 bedGraph or WIG file using UCSC tools or from a BAM file using the
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82 bamCoverage tool. (--scoreFileName)"/>
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83
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84 <conditional name="mode" >
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85 <param name="mode_select" type="select"
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86 label="computeMatrix has two main output options"
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87 help="In the scale-regions mode, all regions in the BED file are
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88 stretched or shrunk to the same length (in bases) that is indicated
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89 by the user. Reference-point refers to a position within the BED
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90 regions (e.g start of region). In the reference-point mode only
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91 those genomic positions before (upstream) and/or after (downstream)
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92 the reference point will be considered.">
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93 <option value="scale-regions" selected="true">scale-regions</option>
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94 <option value="reference-point">reference-point</option>
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95 </param>
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96
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97 <when value="scale-regions" >
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98 <param argument="--regionBodyLength" type="integer" value="500"
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99 label="Distance in bases to which all regions are going to be fit" help=""/>
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100 <conditional name="regionStartLength">
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101 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
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102 <option value="no" selected="true">no</option>
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103 <option value="yes">yes</option>
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104 </param>
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105 <when value="no" />
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106 <when value="yes">
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107 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
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108 label="Distance upstream of the region start position"
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109 help="If the regions are genes, this would be the
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110 distance upstream of the transcription start site."/>
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111 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
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112 label="Distance downstream of the region end position"
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113 help="If the regions are genes, this would be the
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114 distance downstream of the transcription end site."/>
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115 </when>
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116 </conditional>
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117 </when>
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118 <when value="reference-point">
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119 <param name="referencePoint" type="select" label="The reference point for the plotting">
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120 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
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121 <option value="TES">end of region (e.g. TES)</option>
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122 <option value="center">center of region</option>
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123 </param>
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124 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue=""
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125 label="Discard any values after the region end"
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126 help="This is useful to visualize the region end when not using the
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127 scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/>
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128 <param name="beforeRegionStartLength" type="integer" value="1000" min="1"
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129 label="Distance upstream of the start site of the regions defined in the region file"
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130 help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/>
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131 <param name="afterRegionStartLength" type="integer" value="1000" min="1"
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132 label="Distance downstream of the end site of the given regions"
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133 help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/>
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134 </when>
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135 </conditional>
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136
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137 <expand macro="input_graphic_output_settings">
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138 <expand macro="input_save_matrix_values" />
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139 </expand>
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140
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141 <conditional name="advancedOpt" >
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142 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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143 <option value="no" selected="true">no</option>
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144 <option value="yes">yes</option>
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145 </param>
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146 <when value="no" />
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147 <when value="yes">
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148 <param name="binSize" type="integer" value="50" min="1"
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149 label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
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150 help="(--binSize)"/>
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151
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152 <expand macro="sortRegions" />
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153 <expand macro="sortUsing" />
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154
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155 <param name="averageTypeBins" type="select"
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156 label="Define the type of statistic that should be displayed."
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157 help="The value is computed for each bin. (--averageTypeBins)">
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158 <option value="mean" selected="true">mean</option>
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159 <option value="median">median</option>
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160 <option value="min">min</option>
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161 <option value="max">max</option>
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162 <option value="sum">sum</option>
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163 <option value="std">std</option>
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164 </param>
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165
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166 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
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167 label="Convert missing values to 0?."
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168 help="If set to 'yes', missing values (NAs) are converted to 0.
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169 The default is to ignore such cases, which will be
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170 depicted as black areas once a heatmap is created." />
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171
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172 <expand macro="skipZeros" />
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173 <expand macro="skipNAs" />
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174
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175 <param name="minThreshold" type="float" optional="True"
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176 label="Minimum threshold"
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177 help="Any region containing a value that is equal or less than this numeric
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178 value will be skipped. This is useful to skip, for example, genes where the
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179 read count is zero for any of the bins. This could be the result of
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180 unmappable areas and can bias the overall results. (--minThreshold)"/>
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181 <param name="maxThreshold" type="float" optional="True"
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182 label="Maximum threshold"
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183 help="Any region containing a value that is equal or higher that this
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184 numeric value will be skipped. The max threshold is useful to skip those
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185 few regions with very high read counts (e.g. major satellites) that may
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186 bias the average values. (--maxThreshold)"/>
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187 <param name="scale" type="float" optional="True" label="Scaling factor"
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188 help="If set, all values are multiplied by this number. (--scale)"/>
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189 </when>
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190 </conditional>
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191 </inputs>
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192 <outputs>
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193 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
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194 <expand macro="output_graphic_outputs" />
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195 <expand macro="output_save_matrix_values" />
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196 </outputs>
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197 <!--
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198 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
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199 -->
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200 <tests>
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201 <test>
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202 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
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203 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
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204 <param name="showAdvancedOpt" value="yes" />
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205 <param name="mode_select" value="reference-point" />
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206 <param name="binSize" value="10" />
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207 <param name="sortUsing" value="sum" />
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208 <param name="averageTypeBins" value="sum" />
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209 <param name="skipNAs" value="False" />
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210 <param name="beforeRegionStartLength" value="10" />
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211 <param name="afterRegionStartLength" value="10" />
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212 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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213 </test>
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214 <test>
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215 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
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216 <param name="scoreFileName" value="computeMatrix2.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="beforeRegionStartLength" value="10" />
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221 <param name="afterRegionStartLength" value="10" />
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222 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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223 </test>
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224 <test>
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225 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
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226 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
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227 <param name="showAdvancedOpt" value="yes" />
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228 <param name="mode_select" value="scale-regions" />
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229 <param name="endLabel" value="END" />
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230 <param name="regionStartLength" value="yes" />
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231 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
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232 </test>
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233 </tests>
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234 <help>
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235 <![CDATA[
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236 **What it does**
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237
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238 This tool prepares an intermediate file (a gzipped table of values)
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239 that contains scores associated with genomic regions and can be used
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240 afterwards to plot a heatmap or profile.
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241
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242 Genomic regions can really be anything - genes, parts of genes, ChIP-seq
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243 peaks, favorite genome regions... as long as you provide a proper file
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244 in BED or INTERVAL format. If you would like to compare different groups of regions
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245 (i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.
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246
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247 computeMatrix can also be used to filter and sort
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248 regions according to their score by making use of its advanced output options.
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249
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250
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251 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
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252 :alt: Relationship between computeMatrix, heatmapper and profiler
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253
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254
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255 You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeMatrix.html
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256
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257
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258 -----
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259
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260 @REFERENCES@
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261 ]]>
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262 </help>
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263 <expand macro="citations" />
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264 </tool>