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