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annotate bigwigCompare.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
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1 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="@WRAPPER_VERSION@.0">
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2 <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</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 bigwigCompare
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12 @THREADS@
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13
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14 --bigwig1 '$bigwigFile1'
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15 --bigwig2 '$bigwigFile2'
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16
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17 --outFileName '$outFileName'
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18 --outFileFormat '$outFileFormat'
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19
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20 --ratio $comparison.comparison_select
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21
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22 #if $comparison.comparison_select in ['ratio','log2']:
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23 --pseudocount $comparison.pseudocount
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24 #end if
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25
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26 #if str($region).strip() != '':
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27 --region '$region'
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28 #end if
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29
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30 #if $advancedOpt.showAdvancedOpt == "yes":
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31
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32 --missingDataAsZero $advancedOpt.missingDataAsZero
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33 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
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34 --binSize $advancedOpt.binSize
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35
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36 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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37 --plotTitle '$advancedOpt.plotTitle'
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38 #end if
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39
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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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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 fold changes. (--ratio)">
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53 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
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54 <option value="ratio">compute the ratio of the number of reads</option>
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55 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
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56 <option value="add">compute the sum over all reads</option>
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57 <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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58 </param>
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59 <when value="log2">
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60 <expand macro="pseudocount" />
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61 </when>
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62 <when value="ratio">
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63 <expand macro="pseudocount" />
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64 </when>
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65 <when value="subtract" />
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66 <when value="add" />
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67 <when value="reciprocal_ratio">
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68 <expand macro="pseudocount" />
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69 </when>
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70 </conditional>
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72 <param name="outFileFormat" type="select" label="Coverage file format">
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73 <option value="bigwig" selected="true">bigwig</option>
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74 <option value="bedgraph">bedgraph</option>
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75 </param>
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77 <expand macro="region_limit_operation" />
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79 <conditional name="advancedOpt">
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80 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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81 <option value="no" selected="true">no</option>
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82 <option value="yes">yes</option>
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83 </param>
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84 <when value="no" />
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85 <when value="yes">
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86 <param name="binSize" type="integer" value="50" min="1"
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87 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length"
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88 help="Size of the bins in bp for the output of the bigwig/bedgraph file. (--binSize)"/>
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89 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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90 label ="Treat missing data as zero"
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91 help ="This parameter determines if missing data should be replaced with a zero.
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92 If set to &quot;no&quot;, missing data will be ignored and will not be included in the
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93 output file at all. Missing data is defined as those regions for which no value exists in
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94 *any* of the bigwig files. The decision to include or exclude missing data depends on
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95 the interpretation of the data. Missing data in a bigwig file may mean that there is no
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96 information available for certain regions, for example a repetitive region that is not
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97 being considered. In the same file regions with low coverage may get zero read counts.
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98 If missing data is replaced by zero, this would convert the excluded repetitive regions
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99 into regions of low coverage. (--missingDataAsZero)" />
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100 <expand macro="scaleFactor" />
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101 <expand macro="plotTitle" />
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102 </when>
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103 </conditional>
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104 </inputs>
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105 <outputs>
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106 <data format="bigwig" name="outFileName">
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107 <change_format>
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108 <when input="outFileFormat" value="bigwig" format="bigwig" />
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109 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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110 </change_format>
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111 </data>
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112 </outputs>
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113 <tests>
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114 <test>
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115 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
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116 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
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117 <param name="showAdvancedOpt" value="no" />
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118 <param name="outFileFormat" value="bigwig" />
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119 <param name="binSize" value="5" />
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120 <param name="comparison_select" value="ratio" />
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121 <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
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122 </test>
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123 <test>
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124 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
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125 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
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126 <param name="showAdvancedOpt" value="no" />
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127 <param name="outFileFormat" value="bedgraph" />
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128 <param name="binSize" value="10" />
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129 <param name="comparison_select" value="ratio" />
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130 <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" />
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131 </test>
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132 </tests>
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133 <help>
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134 <![CDATA[
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135 **What it does**
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136
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137 This tool compares two bigwig files based on the number of mapped reads. To
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138 compare the bigwig files the genome is partitioned into bins of equal size,
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139 then the number of reads found in each BAM file are counted for such bins and
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140 finally a summarizing value is reported. This value can be the ratio of the
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141 number of reads per bin, the log2 of the ratio, the sum or the difference.
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142
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143
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144 -----
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145
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146 @REFERENCES@
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147 ]]>
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148 </help>
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149 <expand macro="citations" />
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150 </tool>