Mercurial > repos > bgruening > deeptools_multi_bam_summary

annotate multiBamSummary.xml @ 31:d9e59cf2fdf6 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 13:42:02 +0000
parents a1a84914d00d
children
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31
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1 <tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
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2 <description>calculates average read coverages for a list of two or more BAM/CRAM files</description>
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3 <macros>
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4 <token name="@BINARY@">multiBamSummary</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 #set files=[]
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11 #set labels=[]
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12
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13 @multiple_input_bams@
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14 @BINARY@
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15 $mode.modeOpt
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16 @THREADS@
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18 --outFileName '$outFile'
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19 --bamfiles #echo " ".join($files)#
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20 --labels #echo " ".join($labels)#
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22 #if $outRawCounts:
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23 --outRawCounts '$outFileRawCounts'
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24 #end if
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25
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26 #if $scalingFactors:
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27 --scalingFactors '$scalingFactorsFile'
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28 #end if
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29
0
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30 #if $mode.modeOpt == "bins":
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31 --binSize '$mode.binSize'
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32 --distanceBetweenBins '$mode.distanceBetweenBins'
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33 #else:
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34 --BED $mode.region_file
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35 #end if
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37 #if str($region).strip() != '':
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38 --region '$region'
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39 #end if
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40
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41 #if $advancedOpt.showAdvancedOpt == "yes":
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42 @ADVANCED_OPTS_READ_PROCESSING@
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43 @ADVANCED_OPTS_GTF@
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44 @blacklist@
0
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45 #end if
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46 ]]>
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47 </command>
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48
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49 <inputs>
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50 <expand macro="multiple_input_bams" MIN="2"/>
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51 <expand macro="custom_sample_labels" />
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52
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53 <conditional name="mode">
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54 <param name="modeOpt" type="select" label="Choose computation mode"
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55 help="In the bins mode, the coverage is computed for equally
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56 sized bins. \nIn BED file mode, a list of genomic regions
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57 in BED or INTERVAL format has to be given. For each region
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58 in the BED file, the number of overlapping reads from each BAM file is counted.
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59 ">
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60 <option value="bins" selected="true">Bins</option>
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61 <option value="BED-file">Limit calculation to certain regions (BED file)</option>
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62 </param>
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63 <when value="bins">
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64 <param name="binSize" type="integer" value="10000" min="1"
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65 label="Bin size in bp"
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66 help="Length in bases of the window used to sample the genome. (--binSize)"/>
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67
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68 <expand macro="distanceBetweenBins" />
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69
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70 </when>
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71 <when value="BED-file">
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72 <param name="region_file" type="data" format="bed,gtf"
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73 label="Region file in BED or INTERVAL format"
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74 help="Coverage is computed for the number of reads that overlap such regions."/>
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75 </when>
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76 </conditional>
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77
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78 <expand macro="region_limit_operation" />
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79
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80 <expand macro="advancedOpt_scaffold">
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81 <expand macro="read_processing_options" />
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82 <expand macro="gtf_options" />
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83 <expand macro="blacklist" />
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84 </expand>
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85
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86 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
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87 <param argument="--scalingFactors" type="boolean" label="Save scaling factors" help="Scaling factors calculated as in DESeq2 and made directly compatible with bamCoverage."/>
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88
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89 </inputs>
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90 <outputs>
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91 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
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92 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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93 <filter>outRawCounts is True</filter>
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94 </data>
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95 <data format="tabular" name="scalingFactorsFile" label="${tool.name} on ${on_string}: scaling factors">
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96 <filter>scalingFactors is True</filter>
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97 </data>
0
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98 </outputs>
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99 <tests>
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100 <test>
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101 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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102 <param name="modeOpt" value="bins" />
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103 <param name="binSize" value="10" />
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104 <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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105 </test>
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106 <test>
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107 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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108 <param name="modeOpt" value="BED-file" />
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109 <param name="region_file" value="multiBamSummary_regions.bed" />
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110 <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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111 </test>
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112
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113
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114 </tests>
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115 <help>
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116 <![CDATA[
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117
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118 What it does
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119 -------------
0
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120
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121 This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files).
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122 The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted.
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123 Alternatively, an interval file with pre-defined genomic regions can be provided.
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124
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125 In principle, this tool does the same as ``multiBigwigSummary``, but for BAM files.
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126
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127 A typical follow-up application is to check and visualize the similarity and variability between replicates or published data sets (see: ``plotPCA`` and ``plotCorrelation``).
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128
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129 Output
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130 --------
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131
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132 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.
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133
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134 To analyze the coverage 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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135
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136 .. image:: $PATH_TO_IMAGES/multiBamSummary_output.png
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137 :width: 600
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138 :height: 443
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139
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140 -----
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141
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142 @REFERENCES@
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143 ]]>
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144 </help>
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145 <expand macro="citations" />
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146 </tool>