Mercurial > repos > bgruening > deeptools_multi_bigwig_summary
annotate multiBigwigSummary.xml @ 3:e58ad44b9249 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author | bgruening |
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date | Wed, 09 Mar 2016 18:10:05 -0500 |
parents | 3da3c3750962 |
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bb542efec3b7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0"> |
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3da3c3750962
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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2 <description>calculates average scores for a list of two or more bigwig files</description> |
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3 <macros> |
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4 <token name="@BINARY@">multiBigwigSummary</token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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5 <import>deepTools_macros.xml</import> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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6 </macros> |
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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8 <command> |
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9 <![CDATA[ |
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10 #set files=[] |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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11 #set labels=[] |
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12 |
bb542efec3b7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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13 @multiple_input_bigwigs@ |
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14 |
bb542efec3b7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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15 @BINARY@ |
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16 $mode.modeOpt |
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17 |
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18 @THREADS@ |
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19 |
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20 --outFileName $outFile |
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21 --bwfiles '#echo "' '".join($files)#' |
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22 --labels '#echo "' '".join($labels)#' |
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23 |
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24 #if $outRawCounts: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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25 --outRawCounts '$outFileRawCounts' |
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26 #end if |
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27 |
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28 #if $mode.modeOpt == "bins": |
bb542efec3b7
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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29 --binSize '$mode.binSize' |
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30 --distanceBetweenBins '$mode.distanceBetweenBins' |
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31 #else: |
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32 --BED $mode.region_file |
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33 #end if |
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34 |
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35 #if str($region.value) != '': |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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36 --region '$region' |
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37 #end if |
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38 ]]> |
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39 </command> |
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40 |
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41 <inputs> |
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42 <expand macro="multiple_input_bigwigs" /> |
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43 |
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44 <conditional name="mode"> |
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45 <param name="modeOpt" type="select" label="Choose computation mode" |
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46 help="In the bins mode, the correlation is computed using equally sized bins. |
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47 In the BED file mode, a list of genomic regions in BED format has to be given. |
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48 For each region in the BED file, the number of overlapping reads is counted in |
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49 each of the BigWig files. Then the correlation is computed."> |
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50 <option value="bins" selected="true">Bins</option> |
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51 <option value="BED-file">Limit correlation to certain regions (BED file)</option> |
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52 </param> |
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53 <when value="bins"> |
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54 <param name="binSize" type="integer" value="10000" min="1" |
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55 label="Bin size in bp" |
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56 help="Length in bases for a window used to sample the genome. (--binSize)"/> |
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57 |
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58 <expand macro="distanceBetweenBins" /> |
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59 </when> |
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60 <when value="BED-file"> |
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61 <param name="region_file" type="data" format="bed" |
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62 label="Region file in BED format" |
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63 help="Correlation is computed for the number of reads that overlap such regions."/> |
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64 </when> |
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65 </conditional> |
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66 |
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67 <expand macro="region_limit_operation" /> |
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68 <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/> |
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69 |
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70 </inputs> |
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71 <outputs> |
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72 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" /> |
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73 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> |
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74 <filter>outRawCounts is True</filter> |
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75 </data> |
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76 </outputs> |
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77 <tests> |
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78 <test> |
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79 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" /> |
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80 <param name="modeOpt" value="bins" /> |
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81 <param name="binSize" value="10" /> |
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82 <param name="corMethod" value="spearman" /> |
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83 <output name="outFileName" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> |
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84 </test> |
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85 <!--test> |
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86 <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" /> |
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87 <param name="modeOpt" value="BED-file" /> |
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88 <param name="region_file" value="multiBamSummary_regions.bed" /> |
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89 <param name="corMethod" value="pearson" /> |
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90 <param name="outRawCounts" value="True" /> |
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91 <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" /> |
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92 <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> |
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93 </test--> |
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94 </tests> |
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95 <help> |
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96 <![CDATA[ |
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97 |
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98 What it does |
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99 -------------- |
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100 |
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101 This tool computes the average scores for every genomic region for every bigWig file that is provided. In principle, it does the same as ``multiBamSummary``, but for bigWig files. |
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102 |
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103 The analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions (e.g., genes) in 'BED-file' mode. |
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104 |
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105 Typically the output of ``multiBigwigSummary`` is used by other tools, such as ``plotCorrelation`` or ``plotPCA``, for visualization and diagnostic purposes. |
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106 |
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107 |
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108 Output |
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109 -------- |
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110 |
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111 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``. |
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112 |
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113 To analyze the average scores yourself, you can get the **uncompressed score matrix** where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file). (To obtain this output file, select "Save raw counts (coverages) to file" ) |
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114 |
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115 .. image:: $PATH_TO_IMAGES/multiBigwigSummary_output.png |
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116 :width: 600 |
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117 :height: 358 |
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118 |
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119 ----- |
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120 |
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121 @REFERENCES@ |
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122 ]]> |
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123 </help> |
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124 <expand macro="citations" /> |
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125 </tool> |