Mercurial > repos > bgruening > deeptools
annotate bamCorrelate.xml @ 31:7889d260cc37 draft default tip
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
| author | bgruening |
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| date | Wed, 21 Oct 2015 02:50:24 -0400 |
| parents | 5231f398d784 |
| children |
| rev | line source |
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| 28 | 1 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0"> |
| 26 | 2 <description>correlates pairs of BAM files</description> |
| 3 <macros> | |
| 4 <token name="@BINARY@">bamCorrelate</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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7 <expand macro="requirements" /> |
| 26 | 8 <command> |
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9 <![CDATA[ |
| 26 | 10 #set files=[] |
| 11 #set labels=[] | |
| 12 | |
| 13 @multiple_input_bams@ | |
| 14 | |
| 15 bamCorrelate | |
| 16 | |
| 17 $mode.modeOpt | |
| 18 | |
| 19 @THREADS@ | |
| 20 | |
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21 --bamfiles '#echo "' '".join($files)#' |
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5231f398d784
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22 --labels '#echo "' '".join($labels)#' |
| 26 | 23 --fragmentLength $fragmentLength |
| 24 --corMethod $corMethod | |
| 25 | |
| 26 --plotFile $outFileName | |
| 27 | |
| 28 #if $output.showOutputSettings == "yes" | |
| 29 --outRawCounts '$outFileRawCounts' | |
| 30 --outFileCorMatrix '$outFileCorMatrix' | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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31 --plotFileFormat '$output.outFileFormat' |
| 26 | 32 #else: |
| 33 --plotFileFormat 'png' | |
| 34 #end if | |
| 35 | |
| 36 #if $mode.modeOpt == "bins": | |
| 37 --binSize '$mode.binSize' | |
| 28 | 38 --distanceBetweenBins '$mode.distanceBetweenBins' |
| 39 $mode.doNotRemoveOutliers | |
| 26 | 40 #else: |
| 41 --BED $mode.region_file | |
| 42 #end if | |
| 43 | |
| 44 #### options available in both modes | |
| 45 #if str($mode.region.value) != '': | |
| 46 --region '$mode.region' | |
| 47 #end if | |
| 48 | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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49 #if $plotTitle and str($plotTitle).strip() != "": |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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50 --plotTitle '$plotTitle' |
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5231f398d784
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51 #end if |
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5231f398d784
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52 $plotNumbers |
| 26 | 53 #if $mode.advancedOpt.showAdvancedOpt == "yes": |
| 54 | |
| 55 $mode.advancedOpt.doNotExtendPairedEnds | |
| 56 $mode.advancedOpt.ignoreDuplicates | |
| 57 $mode.advancedOpt.includeZeros | |
| 58 | |
| 59 #if $mode.advancedOpt.minMappingQuality: | |
| 60 --minMappingQuality '$mode.advancedOpt.minMappingQuality' | |
| 61 #end if | |
| 62 | |
| 63 #if $mode.advancedOpt.zMin: | |
| 64 --zMin $mode.advancedOpt.zMin | |
| 65 #end if | |
| 66 #if $mode.advancedOpt.zMax: | |
| 67 --zMax $mode.advancedOpt.zMax | |
| 68 #end if | |
| 69 --colorMap '$mode.advancedOpt.colorMap' | |
| 70 | |
| 71 #end if | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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72 ]]> |
| 26 | 73 </command> |
| 74 | |
| 75 <inputs> | |
| 76 <expand macro="multiple_input_bams" /> | |
| 77 | |
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78 <param name="fragmentLength" type="integer" value="200" min="1" |
| 26 | 79 label="Length of the average fragment size" |
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80 help ="Reads will be extended to match this length unless they are paired-end, |
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5231f398d784
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81 in which case they will be extended to match the fragment length. |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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82 *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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83 be extended to match the fragment length. (--fragmentLength)"/> |
| 26 | 84 |
| 85 <param name="corMethod" type="select" label="Correlation method"> | |
| 28 | 86 <option value="spearman" selected="True">Spearman</option> |
| 26 | 87 <option value="pearson">Pearson</option> |
| 88 </param> | |
| 89 | |
| 90 <conditional name="mode"> | |
| 91 <param name="modeOpt" type="select" label="Choose computation mode" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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92 help="In the bins mode, the correlation is computed based on equal |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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93 length bins. In the BED file mode, as list of genomic regions in BED |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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94 format has to be given. For each region in the BED file the number of |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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95 overlapping reads is counted in each of the BAM files. |
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5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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96 Then the correlation is computed."> |
| 26 | 97 <option value="bins" selected="true">Bins</option> |
| 98 <option value="BED-file">Limit correlation to certain regions (BED file)</option> | |
| 99 </param> | |
| 100 <when value="bins"> | |
| 101 <param name="binSize" type="integer" value="10000" min="1" | |
| 102 label="Bin size in bp" | |
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103 help="Length in base pairs for a window used to sample the genome. (--binSize)"/> |
| 26 | 104 |
| 28 | 105 <param name="distanceBetweenBins" type="integer" value="0" min="0" |
| 106 label="Distance between bins" | |
| 107 help="By default, bamCorrelate considers consecutive bins of | |
| 108 the specified 'Bin size'. However, to reduce the | |
| 109 computation time, a larger distance between bins can | |
| 110 by given. Larger distances result in less bins being | |
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111 considered. (--distanceBetweenBins)"/> |
| 28 | 112 |
| 113 <param name="doNotRemoveOutliers" type="boolean" | |
| 114 truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers" | |
| 115 help="By default, bins with very large counts are removed. | |
| 116 By setting this option, outliers will not be | |
| 117 removed. Bins with unusually large counts normally | |
| 118 correspond to regions in the genome that accumulate | |
| 119 lot of reads like satellite regions. If outliers are not | |
| 120 removed the pearson correlation will wrongly report a | |
| 121 very high correlation; that's why, by default, | |
| 122 bamCorrelate tries to remove outliers using | |
| 123 the median absolute deviation (MAD) method applying a | |
| 124 threshold of 200 to only consider extremely large | |
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125 deviations from the median. (--doNotRemoveOutliers)"/> |
| 28 | 126 |
| 26 | 127 <expand macro="bamCorrelate_mode_actions" /> |
| 128 </when> | |
| 129 <when value="BED-file"> | |
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130 <param name="region_file" type="data" format="bed" |
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131 label="Region file in BED format" |
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132 help="Correlation is computed for the number of reads that overlap such regions."/> |
| 26 | 133 <expand macro="bamCorrelate_mode_actions" /> |
| 134 </when> | |
| 135 </conditional> | |
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136 <expand macro="plotTitle" /> |
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137 <expand macro="plotNumbers" /> |
| 26 | 138 <conditional name="output"> |
| 139 <param name="showOutputSettings" type="select" label="Show advanced output settings" > | |
| 140 <option value="no" selected="true">no</option> | |
| 141 <option value="yes">yes</option> | |
| 142 </param> | |
| 143 <when value="no" /> | |
| 144 <when value="yes"> | |
| 145 <expand macro="input_image_file_format"/> | |
| 146 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> | |
| 147 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/> | |
| 148 </when> | |
| 149 </conditional> | |
| 150 | |
| 151 </inputs> | |
| 152 <outputs> | |
| 153 <expand macro="output_image_file_format" /> | |
| 154 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> | |
| 155 <filter> | |
| 156 (( | |
| 157 output['showOutputSettings'] == 'yes' and | |
| 158 output['saveRawCounts'] is True | |
| 159 )) | |
| 160 </filter> | |
| 161 </data> | |
| 162 <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix"> | |
| 163 <filter> | |
| 164 (( | |
| 165 output['showOutputSettings'] == 'yes' and | |
| 166 output['saveCorMatrix'] is True | |
| 167 )) | |
| 168 </filter> | |
| 169 </data> | |
| 170 </outputs> | |
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171 <tests> |
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172 <test> |
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173 <repeat name="input_files"> |
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174 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> |
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175 <param name="label" value="first BAM file" /> |
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176 </repeat> |
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177 <repeat name="input_files"> |
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178 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> |
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179 <param name="label" value="second BAM file" /> |
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180 </repeat> |
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181 <param name="modeOpt" value="bins" /> |
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182 <param name="binSize" value="10" /> |
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183 <param name="showOutputSettings" value="no" /> |
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184 <output name="outFileName" file="bamCorrelate_result1.png" ftype="png" compare="sim_size" /> |
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185 </test> |
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186 </tests> |
| 26 | 187 <help> |
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188 <![CDATA[ |
| 26 | 189 **What it does** |
| 190 | |
| 191 This tool is useful to assess the overall similarity of different BAM files. A typical application | |
| 192 is to check the correlation between replicates or published data sets. | |
| 193 | |
| 194 The tool splits the genomes into bins of given length. For each bin, the number of reads | |
| 195 found in each BAM file is counted and a correlation (either Pearson or Spearman) is computed for all | |
| 196 pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples. | |
| 197 | |
| 198 | |
| 199 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png | |
| 200 :alt: Heatmap of RNA Polymerase II ChIP-seq | |
| 201 | |
| 202 | |
| 203 You can find more details on the bamCorrelate wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate | |
| 204 | |
| 205 | |
| 206 **Output files**: | |
| 207 | |
| 208 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example | |
| 209 - data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used | |
| 210 | |
| 211 | |
| 212 ----- | |
| 213 | |
| 214 @REFERENCES@ | |
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215 ]]> |
| 26 | 216 </help> |
| 29 | 217 <expand macro="citations" /> |
| 26 | 218 </tool> |