Mercurial > repos > bgruening > deeptools_plot_coverage

comparison plotCoverage.xml @ 9:4679da05d86c draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
author bgruening
date Mon, 15 Feb 2016 10:06:17 -0500
parents 1a6309cecf71
children 752d2d85e6af
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8:02331b8ed2e8 9:4679da05d86c
1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
2 <description>plots a histogram of coverage on genomic regions </description> 2 <description>assesses the sequencing depth of BAM files </description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">plotCoverage</token> 4 <token name="@BINARY@">plotCoverage</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"/>
80 <!--param name="outFileFormat" value="png" /--> 80 <!--param name="outFileFormat" value="png" /-->
81 <param name="showAdvancedOpt" value="yes" /> 81 <param name="showAdvancedOpt" value="yes" />
82 <param name="plotTitle" value="Test Title from Galaxy" /> 82 <param name="plotTitle" value="Test Title from Galaxy" />
83 <param name="outRawCounts" value="True" /> 83 <param name="outRawCounts" value="True" />
84 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" /> 84 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
85 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="100" /> 85 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="500" />
86 </test> 86 </test>
87 </tests> 87 </tests>
88 <help> 88 <help>
89 <![CDATA[ 89 <![CDATA[
90 **What it does** 90 What it does
91 -------------
91 92
92 This tools samples 1 million positions in the genome to build 93 This tool is useful to **assess the sequencing depth** of a given sample.
93 a coverage histogram. Multiple bam files are accepted but all should 94 It samples 1 million bp, counts the number of overlapping reads and reports
94 correspond to the same genome assembly. 95 a coverage histogram that tells you how many bases are covered how many times.
96
97 **Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.
98
99 Output
100 ---------
101
102 The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more.
103
104 The optional output is a table where each row represents the number of reads overlapping with a sampled bp.
105
106 .. image:: $PATH_TO_IMAGES/plotCoverage_output.png
107 :width: 600
108 :height: 345
109
110 Example plot
111 -----------------
112
113 .. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
114 :width: 600
115 :height: 291
95 116
96 117
97 @REFERENCES@ 118 @REFERENCES@
98 ]]> 119 ]]>
99 </help> 120 </help>