Mercurial > repos > bgruening > deeptools_multi_bam_summary

comparison multiBamSummary.xml @ 1:f2a582e0314d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:27:26 -0500
parents 04b612e24e62
children b319edc108a7
comparison
equal deleted inserted replaced
0:04b612e24e62 1:f2a582e0314d
39 #end if 39 #end if
40 ]]> 40 ]]>
41 </command> 41 </command>
42 42
43 <inputs> 43 <inputs>
44 <expand macro="multiple_input_bams" /> 44 <expand macro="multiple_input_bams_min2" />
45 45
46 <conditional name="mode"> 46 <conditional name="mode">
47 <param name="modeOpt" type="select" label="Choose computation mode" 47 <param name="modeOpt" type="select" label="Choose computation mode"
48 help="In the bins mode, the coverage is computed for equally 48 help="In the bins mode, the coverage is computed for equally
49 sized bins. In the BED file mode, a list of genomic regions in BED 49 sized bins. \nIn BED file mode, a list of genomic regions
50 format has to be given. For each region in the BED file the number of 50 in BED or INTERVAL format has to be given. For each region
51 overlapping reads is counted in each of the BAM files. 51 in the BED file, the number of overlapping reads from each BAM file is counted.
52 "> 52 ">
53 <option value="bins" selected="true">Bins</option> 53 <option value="bins" selected="true">Bins</option>
54 <option value="BED-file">Limit calculation to certain regions (BED file)</option> 54 <option value="BED-file">Limit calculation to certain regions (BED file)</option>
55 </param> 55 </param>
56 <when value="bins"> 56 <when value="bins">
61 <expand macro="distanceBetweenBins" /> 61 <expand macro="distanceBetweenBins" />
62 62
63 </when> 63 </when>
64 <when value="BED-file"> 64 <when value="BED-file">
65 <param name="region_file" type="data" format="bed" 65 <param name="region_file" type="data" format="bed"
66 label="Region file in BED format" 66 label="Region file in BED or INTERVAL format"
67 help="Coverage is computed for the number of reads that overlap such regions."/> 67 help="Coverage is computed for the number of reads that overlap such regions."/>
68 </when> 68 </when>
69 </conditional> 69 </conditional>
70 70
71 <expand macro="region_limit_operation" /> 71 <expand macro="region_limit_operation" />
100 100
101 </tests> 101 </tests>
102 <help> 102 <help>
103 <![CDATA[ 103 <![CDATA[
104 104
105 **What it does** 105 What it does
106 -------------
106 107
107 This tool generates a matrix of read-coverages for a list of genomic regions and at least two samples (BAM files). 108 This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files).
108 The genome is split into bins of the given size. For each bin, the number of reads found in it in each BAM file is counted. 109 The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted.
109 Alternatively, a bed file with pre-defined genomic regions can be provided. In each case the calculation can further be limited to 110 Alternatively, an interval file with pre-defined genomic regions can be provided.
110 a given genomic interval (e.g. a given chromosome). This option is mostly used for testing and efficiency.
111 A typical follow-up application is to check and visualize the similarity between replicates or published data sets (see: plotPCA and plotCorrelation).
112 111
113 **Output files**: 112 In principle, this tool does the same as ``multiBigwigSummary``, but for BAM files.
114 113
115 - **score matrix**: a compressed matrix where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file) 114 A typical follow-up application is to check and visualize the similarity and variability between replicates or published data sets (see: ``plotPCA`` and ``plotCorrelation``).
116 - Optional : Uncompressed **score matrix**, in case you want to analyse the coverage scores yourself. (Select to "Save raw counts" from above)
117 115
118 ======= 116 Output
117 --------
119 118
120 .. image:: $PATH_TO_IMAGES/QC_multiBamSummary_humanSamples.png 119 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.
121 :alt: Heatmap of RNA Polymerase II ChIP-seq
122 120
121 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" )
123 122
124 You can find more details on the multiBamSummary doc page: https://deeptools.readthedocs.org/en/master/content/tools/multiBamSummary.html 123 .. image:: $PATH_TO_IMAGES/multiBamSummary_output.png
124 :width: 600
125 :height: 443
125 126
126 ----- 127 -----
127 128
128 @REFERENCES@ 129 @REFERENCES@
129 ]]> 130 ]]>