Mercurial > repos > bgruening > deeptools_bigwig_compare

annotate bigwigCompare.xml @ 43:b1ee75d72eee draft default tip

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:25:43 +0000
parents 26031beab653
children
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1 <tool id="deeptools_bigwig_compare" name="bigwigCompare" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
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2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them</description>
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3 <macros>
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4 <token name="@BINARY@">bigwigCompare</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 @BINARY@
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11 @THREADS@
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12 --bigwig1 '$bigwigFile1'
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13 --bigwig2 '$bigwigFile2'
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15 --outFileName '$outFileName'
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16 --outFileFormat '$outFileFormat'
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18 --operation $comparison.comparison_select
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20 #if $comparison.comparison_select in ['ratio','log2']:
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21 --pseudocount $comparison.pseudocount
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22 #end if
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24 #if str($region).strip() != '':
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25 --region '$region'
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26 #end if
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28 #if $advancedOpt.showAdvancedOpt == "yes":
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30 $advancedOpt.skipNAs
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31 $advancedOpt.skipZeroOverZero
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32 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
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33 --binSize $advancedOpt.binSize
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35 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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36 --plotTitle '$advancedOpt.plotTitle'
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37 #end if
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38 @blacklist@
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40 #end if
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41 ]]>
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42 </command>
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43 <inputs>
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44 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
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45 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
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46
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47 <conditional name="comparison">
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48 <param name="comparison_select" type="select"
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49 label="How to compare the two files"
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50 help="The default is to output the log2ratio between the two samples.
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51 The reciprocal ratio returns the negative of the inverse of the ratio if
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52 the ratio is less than 0. The resulting values are interpreted as negative
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53 fold changes. To output the scaled values from the first or second bigWig file,
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54 select 'first' or 'second'.">
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55 <option value="log2" selected="true">Compute log2 of the signal ratio</option>
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56 <option value="ratio">Compute the ratio signals</option>
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57 <option value="subtract">Compute difference (subtract input from treatment) of the signal</option>
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58 <option value="add">Compute the sum of the signals</option>
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59 <option value="mean">Compute the mean of the signal in the two files</option>
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60 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
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61 <option value="first">Returns the scaled value of the first bigWig file</option>
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62 <option value="second">Returns the scaled value of the second bigWig file</option>
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63 </param>
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64 <when value="log2">
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65 <expand macro="pseudocount" />
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66 </when>
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67 <when value="ratio">
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68 <expand macro="pseudocount" />
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69 </when>
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70 <when value="subtract" />
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71 <when value="add" />
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72 <when value="mean" />
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73 <when value="first" />
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74 <when value="second" />
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75 <when value="reciprocal_ratio">
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76 <expand macro="pseudocount" />
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77 </when>
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78 </conditional>
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80 <param name="outFileFormat" type="select" label="Coverage file format">
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81 <option value="bigwig" selected="true">bigwig</option>
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82 <option value="bedgraph">bedgraph</option>
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83 </param>
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84
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85 <expand macro="region_limit_operation" />
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87 <conditional name="advancedOpt">
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88 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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89 <option value="no" selected="true">no</option>
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90 <option value="yes">yes</option>
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91 </param>
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92 <when value="no" />
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93 <when value="yes">
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94 <param argument="--binSize" type="integer" value="50" min="1"
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95 label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
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96 help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
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97
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98 <expand macro="skipNAs" />
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99 <expand macro="skipZeroOverZero" />
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100 <expand macro="scaleFactors" />
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101 <expand macro="plotTitle" />
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102 <expand macro="blacklist" />
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103 </when>
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104 </conditional>
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105 </inputs>
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106 <outputs>
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107 <data format="bigwig" name="outFileName">
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108 <change_format>
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109 <when input="outFileFormat" value="bigwig" format="bigwig" />
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110 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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111 </change_format>
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112 </data>
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113 </outputs>
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114 <tests>
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115 <test>
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116 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
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117 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
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118 <param name="showAdvancedOpt" value="no" />
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119 <param name="outFileFormat" value="bigwig" />
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120 <param name="binSize" value="5" />
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121 <param name="comparison_select" value="ratio" />
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122 <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" compare="sim_size" />
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123 </test>
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124 <test>
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125 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
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126 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
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127 <param name="showAdvancedOpt" value="no" />
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128 <param name="outFileFormat" value="bedgraph" />
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129 <param name="binSize" value="10" />
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130 <param name="comparison_select" value="ratio" />
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131 <output name="outFileName" file="bigwigCompare_result2.bg" sort="true" ftype="bedgraph" />
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132 </test>
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133 </tests>
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134 <help>
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135 <![CDATA[
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136
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137 What it does
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138 --------------
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139
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140 This tool compares two bigWig files based on the number of mapped reads. To
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141 compare the bigwig files, the genome is partitioned into bins of equal size,
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142 then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported.
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143 This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference.
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144
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145 Note that you can actually produce a human-readable bedGraph format instead of the compressed bigWig format if you're interested in having a look at the values yourself.
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146
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147 .. image:: $PATH_TO_IMAGES/bigwigCompare_output.png
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148 :width: 600
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149 :height: 436
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150
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151 -----
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152
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153 @REFERENCES@
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154 ]]>
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155 </help>
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156 <expand macro="citations" />
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157 </tool>