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annotate bigwigCorrelate.xml @ 30:5231f398d784 draft

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author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
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30
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1 <tool id="deeptools_bigwigCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
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2 <description>correlates pairs of BigWig files</description>
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3 <macros>
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4 <token name="@BINARY@">bigwigCorrelate</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 #set files=[]
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11 #set labels=[]
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12
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13 @multiple_input_bigwigs@
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14
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15 bigwigCorrelate
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16
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17 $mode.modeOpt
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18
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19 @THREADS@
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20
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21 --bwfiles '#echo "' '".join($files)#'
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22 --labels '#echo "' '".join($labels)#'
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23 #if $filterPercentile:
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24 --filterPercentile $filterPercentile
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25 #end if
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26 --corMethod $corMethod
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27
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28 --plotFile $outFileName
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29
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30 #if $output.showOutputSettings == "yes"
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31 --outRawCounts '$outFileRawCounts'
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32 --outFileCorMatrix '$outFileCorMatrix'
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33 --plotFileFormat '$output.outFileFormat'
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34 #else:
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35 --plotFileFormat 'png'
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36 #end if
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37
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38 #if $mode.modeOpt == "bins":
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39 --binSize '$mode.binSize'
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40 #else:
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41 --BED $mode.region_file
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42 #end if
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43
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44 #### options available in both modes
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45 #if str($region.value) != '':
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46 --region '$region'
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47 #end if
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48
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49 #if $advancedOpt.showAdvancedOpt == "yes":
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50
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51 $advancedOpt.includeZeros
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52
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53 #if $advancedOpt.zMin:
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54 --zMin $advancedOpt.zMin
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55 #end if
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56 #if $advancedOpt.zMax:
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57 --zMax $advancedOpt.zMax
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58 #end if
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59 --colorMap '$advancedOpt.colorMap'
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60
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61 #if $plotTitle and str($plotTitle).strip() != "":
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62 --plotTitle '$plotTitle'
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63 #end if
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64 $plotNumbers
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65
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66 #end if
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67 ]]>
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68 </command>
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69
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70 <inputs>
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71 <expand macro="multiple_input_bigwigs" />
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72
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73 <param name="filterPercentile" type="float" optional="True" value="" min="0.0" max="100.0"
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74 label="Percentile used to filter out extreme outliers"
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75 help ="If not specified, it is automatically set to 99.9 in analyses
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76 using Pearson correlation! This means that values
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77 above that threshold, which consistently occur in all
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78 datasets, will not be taken into account for the
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79 correlation analysis. This behavior can be overridden
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80 by a user specified value from within the 0.0 to 100.0
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81 range. (--filterPercentile)"/>
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82
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83 <param name="corMethod" type="select" label="Correlation method" help="(--corMethod)">
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84 <option value="spearman" selected="True">Spearman</option>
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85 <option value="pearson">Pearson</option>
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86 </param>
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87
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88 <conditional name="mode">
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89 <param name="modeOpt" type="select" label="Choose computation mode"
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90 help="In the bins mode, the correlation is computed based on equal length bins.
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91 In the BED file mode, as list of genomic regions in BED format has to be given.
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92 For each region in the BED file the number of overlapping reads is counted in
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93 each of the BAM files. Then the correlation is computed.">
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94 <option value="bins" selected="true">Bins</option>
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95 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
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96 </param>
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97 <when value="bins">
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98 <param name="binSize" type="integer" value="10000" min="1"
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99 label="Bin size in bp"
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100 help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
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101 </when>
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102 <when value="BED-file">
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103 <param name="region_file" type="data" format="bed"
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104 label="Region file in BED format"
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105 help="Correlation is computed for the number of reads that overlap such regions."/>
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106 </when>
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107 </conditional>
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108
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109 <expand macro="bigwigCorrelate_mode_actions" />
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110 <conditional name="output">
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111 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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112 <option value="no" selected="true">no</option>
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113 <option value="yes">yes</option>
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114 </param>
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115 <when value="no" />
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116 <when value="yes">
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117 <expand macro="input_image_file_format"/>
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118 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
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119 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
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120 </when>
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121 </conditional>
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122
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123 </inputs>
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124 <outputs>
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125 <expand macro="output_image_file_format" />
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126 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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127 <filter>
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128 ((
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129 output['showOutputSettings'] == 'yes' and
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130 output['saveRawCounts'] is True
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131 ))
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132 </filter>
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133 </data>
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134 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
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135 <filter>
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136 ((
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137 output['showOutputSettings'] == 'yes' and
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138 output['saveCorMatrix'] is True
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139 ))
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140 </filter>
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141 </data>
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142 </outputs>
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143 <tests>
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144 <test>
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145 <repeat name="input_files">
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146 <param name="bigwigfile" value="test.bw" ftype="bigwig" />
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147 <param name="label" value="first bigwig file" />
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148 </repeat>
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149 <repeat name="input_files">
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150 <param name="bigwigfile" value="test.bw" ftype="bigwig" />
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151 <param name="label" value="second bigwig file" />
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152 </repeat>
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153 <param name="modeOpt" value="bins" />
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154 <param name="binSize" value="10" />
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155 <param name="showOutputSettings" value="no" />
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156 <param name="corMethod" value="spearman" />
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157 <output name="outFileName" file="bigwigCorrelate_result1.png" ftype="png" compare="sim_size" />
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158 </test>
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159 </tests>
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160 <help>
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161 <![CDATA[
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162 **What it does**
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163
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164 bigwigCorrelate computes the overall similarity between two or more bigWig
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165 files based on coverage means of genomic regions. The correlation analysis
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166 is performed for the entire genome by running the program in 'bins' mode,
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167 or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses
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168 are available to compute correlation coefficients. Results are saved to a
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169 heat map file. Further output files are optional.
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170
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171
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172 **Output files**:
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173
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174 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation
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175 - data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
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176
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177
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178 -----
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179
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180 @REFERENCES@
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181 ]]>
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182 </help>
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183 <expand macro="citations" />
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184 </tool>