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comparison DepthReports.xml @ 0:6b2e640c8c6d

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author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:31:40 -0600
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1 <?xml version="1.0"?>
2
3 <tool id="depth_reports_1" name="Compute depth of sequencing coverage">
4 <description>over targeted regions in a genome</description>
5 <version_string>depth_reports -v</version_string>
6 <command interpreter="perl">depth_reports $__tool_data_path__ -q $input_bam ${target_bed}.bed $out_summary_table $out_poor_coverage_bed $out_depth_graph $out_depth_table $out_mapped_percentile_table $dud_bed</command>
7 <inputs>
8 <param format="bam" name="input_bam" type="data" label="Mapped alignment file"/>
9 <param name="target_bed" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
10 <param format="bed" name="dud_bed" type="data" label="Targeted regions to ignore (known duds)" optional="true" default="/dev/null"/>
11 </inputs>
12 <outputs>
13 <data name="out_summary_table" format="achri_depth_summary_table" label="Depth of coverage summary (mean, median, etc.)"/>
14 <data name="out_poor_coverage_bed" format="bed" label="Low coverage targeted regions"/>
15 <data name="out_depth_graph" format="png" label="Cumulative depth of coverage graph"/>
16 <data name="out_depth_table" format="tabular" label="Number of bases at each depth of coverage"/>
17 <data name="out_mapped_percentile_table" format="tabular" label="Mapped read depth percentiles"/>
18 </outputs>
19
20 <!-- the following code populates the selection from the public capture kit BED datasets available in the local Galaxy installation -->
21 <code file="capture_kits.py"/>
22
23 <tests>
24 <test>
25 <param name="input_bam" value="depth_test.bam" ftype="bam"/>
26 <param name="target_bed" value="brcas.bed" ftype="bed"/>
27 <output name="out_summary_table">
28 <assert_contents>
29 <has_text text="targeted nucleotide bases: 155091"/>
30 <has_text text="bases mapped to targeted regions: 11473773"/>
31 <has_text text="bases with less than 20-fold coverage: 19046"/>
32 </assert_contents>
33 </output>
34 <output name="out_depth_graph" ftype="png"/>
35 </test>
36 </tests>
37
38 <help>
39 This tool reports several statistics describing the depth of coverage of a next-gen sequencing run over its targeted reference genome.
40 These results can be used to assess the quality of the sequencing for SNP calls, etc.
41 </help>
42
43 </tool>