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author kyost
date Fri, 04 May 2018 02:24:47 -0400
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1 <tool id="window_coverage" name="Calculate window coverage" version="0.1.0">
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2 <description> Determines spanning and total read coverage for overlapping windows spanning peaks of interest. </description>
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3 <requirements>
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4 <requirement type="package" version="1.3">samtools</requirement>
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5 <requirement type="package" version="2.27.0.0">bedtools</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 #set input_list = '","'.join( [str( $input.name ) for $input in $input1 ] )
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12 $__tool_directory__/./window_coverage.bash "$input1" "$input_list" "$input2" "$input3" "$output1" "$output2"
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13 ]]></command>
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14 <inputs>
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15 <param type="data" name="input1" format="bam" multiple="true" label="Filtered Bam Files"/>
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16 <param type="data" name="input2" format="bed" label="qPCR Window Bed File"/>
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17 <param type="float" name="input3" value="0.9" label="Coverage Cutoff"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output1" format="bed" label="Coverage Bed File"/>
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21 <data name="output2" format="bed" label="Spanning Fragment Coverage Bed File" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input1" value="Ch1-1.pe.q10.sort.bam.rmdup.filter.bam,Ch13-1.pe.q10.sort.rmdup.filter.bam"/>
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26 <param name="input2" value="qPCR_windows.bed" />
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27 <param name="input3" value="0.9" />
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28 <output name="output1" file="combined.o.coverage"/>
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29 <output name="output2" file="combined.f9.coverage"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 This tools takes a series of bam files and a bed file of overlapping windows spanning peaks of interest and determines the read coverage and spanning fragment coverage for each window.
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34 ]]></help>
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35 <citations>
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36 <citation type="doi">doi:10.1038/nmeth.4663</citation>
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37 </citations>
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38 </tool>