Mercurial > repos > bgruening > deeptools_bigwig_compare

annotate bigwigCompare.xml @ 26:470e6a076c80 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 07:48:06 -0500
parents 7aba4f9904ff
children af9d00228156
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1 <tool id="deeptools_bigwig_compare" 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 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 --ratio $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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29
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30 $advancedOpt.skipNAs
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31 --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
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32 --binSize $advancedOpt.binSize
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34 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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35 --plotTitle '$advancedOpt.plotTitle'
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36 #end if
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37 @blacklist@
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39 #end if
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40 ]]>
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41 </command>
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42 <inputs>
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43 <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
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44 <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
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46 <conditional name="comparison">
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47 <param name="comparison_select" type="select"
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48 label="How to compare the two files"
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49 help="The default is to output the log2ratio between the two samples.
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50 The reciprocal ratio returns the negative of the inverse of the ratio if
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51 the ratio is less than 0. The resulting values are interpreted as negative
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52 fold changes. To output the scaled values from the first or second BAM file,
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53 select 'first' or 'second'.">
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54 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
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55 <option value="ratio">Compute the ratio of the number of reads</option>
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56 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
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57 <option value="add">Compute the sum of number of reads</option>
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58 <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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59 <option value="first">Returns the scaled value of the first BAM file</option>
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60 <option value="second">Returns the scaled value of the second BAM file</option>
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61 </param>
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62 <when value="log2">
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63 <expand macro="pseudocount" />
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64 </when>
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65 <when value="ratio">
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66 <expand macro="pseudocount" />
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67 </when>
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68 <when value="subtract" />
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69 <when value="add" />
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70 <when value="first" />
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71 <when value="second" />
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72 <when value="reciprocal_ratio">
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73 <expand macro="pseudocount" />
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74 </when>
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75 </conditional>
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76
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77 <param name="outFileFormat" type="select" label="Coverage file format">
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78 <option value="bigwig" selected="true">bigwig</option>
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79 <option value="bedgraph">bedgraph</option>
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80 </param>
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81
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82 <expand macro="region_limit_operation" />
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84 <conditional name="advancedOpt">
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85 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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86 <option value="no" selected="true">no</option>
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87 <option value="yes">yes</option>
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88 </param>
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89 <when value="no" />
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90 <when value="yes">
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91 <param argument="--binSize" type="integer" value="50" min="1"
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92 label="Length, in bases, of the non-overlapping bins used for averaging the score over the regions length"
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93 help="Size of the bins in bases for the output of the bigwig/bedgraph file."/>
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94
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95 <expand macro="skipNAs" />
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96 <expand macro="scaleFactors" />
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97 <expand macro="plotTitle" />
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98 <expand macro="blacklist" />
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99 </when>
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100 </conditional>
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101 </inputs>
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102 <outputs>
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103 <data format="bigwig" name="outFileName">
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104 <change_format>
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105 <when input="outFileFormat" value="bigwig" format="bigwig" />
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106 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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107 </change_format>
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108 </data>
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109 </outputs>
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110 <tests>
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111 <test>
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112 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
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113 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
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114 <param name="showAdvancedOpt" value="no" />
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115 <param name="outFileFormat" value="bigwig" />
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116 <param name="binSize" value="5" />
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117 <param name="comparison_select" value="ratio" />
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118 <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
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119 </test>
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120 <test>
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121 <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
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122 <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
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123 <param name="showAdvancedOpt" value="no" />
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124 <param name="outFileFormat" value="bedgraph" />
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125 <param name="binSize" value="10" />
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126 <param name="comparison_select" value="ratio" />
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127 <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" />
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128 </test>
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129 </tests>
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130 <help>
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131 <![CDATA[
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132
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133 What it does
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134 --------------
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135
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136 This tool compares two bigWig files based on the number of mapped reads. To
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137 compare the bigwig files, the genome is partitioned into bins of equal size,
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138 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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139 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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140
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141 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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142
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143 .. image:: $PATH_TO_IMAGES/bigwigCompare_output.png
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144 :width: 600
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145 :height: 436
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146
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147 -----
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148
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149 @REFERENCES@
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150 ]]>
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151 </help>
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152 <expand macro="citations" />
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153 </tool>