Mercurial > repos > bgruening > deeptools_multi_bigwig_summary

comparison multiBigwigSummary.xml @ 1:3da3c3750962 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:28:51 -0500
parents bb542efec3b7
children 7b4732d497a3
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0:bb542efec3b7 1:3da3c3750962
1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
2 <description>calculates average read coverages for a list of two or more bigwig files</description> 2 <description>calculates average scores for a list of two or more bigwig files</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">multiBigwigSummary</token> 4 <token name="@BINARY@">multiBigwigSummary</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
63 help="Correlation is computed for the number of reads that overlap such regions."/> 63 help="Correlation is computed for the number of reads that overlap such regions."/>
64 </when> 64 </when>
65 </conditional> 65 </conditional>
66 66
67 <expand macro="region_limit_operation" /> 67 <expand macro="region_limit_operation" />
68 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/> 68 <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>
69 69
70 </inputs> 70 </inputs>
71 <outputs> 71 <outputs>
72 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" /> 72 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" />
73 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> 73 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
92 <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> 92 <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
93 </test--> 93 </test-->
94 </tests> 94 </tests>
95 <help> 95 <help>
96 <![CDATA[ 96 <![CDATA[
97 **What it does**
98 97
99 Given two or more bigWig files, multiBigwigSummary computes the average scores for each of the files in every genomic region. 98 What it does
100 This analysis is performed for the entire genome by running the program in 'bins' mode, or for certain user selected regions 99 --------------
101 in 'BED-file' mode. Typically the output of multiBigwigSummary is used by other tools, such as 'plotCorrelation' or 'plotPCA', 100
102 for visualization and diagnostic purposes. 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.
102
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.
104
105 Typically the output of ``multiBigwigSummary`` is used by other tools, such as ``plotCorrelation`` or ``plotPCA``, for visualization and diagnostic purposes.
103 106
104 107
105 **Output files**: 108 Output
109 --------
106 110
107 - **Coverage scores**: Coverage scores computed and saved in a format appropriate for 'plotCorrelation' or 'plotPCA'. 111 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``.
108 112
109 - Data matrix (optional,select to save raw counts to a file above): If you want to have a look at the coverage values 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" )
110 or compute statistics yourself using a different program (like R). 114
115 .. image:: $PATH_TO_IMAGES/multiBigwigSummary_output.png
116 :width: 600
117 :height: 358
111 118
112 ----- 119 -----
113 120
114 @REFERENCES@ 121 @REFERENCES@
115 ]]> 122 ]]>