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1 <tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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4
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9 <![CDATA[
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10 bedtools bedpetobam
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11 -mapq $mapq
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12 -i '$input'
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13 -g $genome
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14 > '$output'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
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19 <expand macro="genome" />
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20 <param name="mapq" type="integer" value="255"
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21 label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
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22 help="(-mapq)" />
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23 </inputs>
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24 <outputs>
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25 <data format="bam" name="output" metadata_source="input"/>
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26 </outputs>
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4
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27 <tests>
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28 <test>
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29 <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
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30 <param name="genome" value="mm9.len"/>
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31 <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
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32 </test>
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33 </tests>
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34 <help>
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35 <![CDATA[
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36 **What it does**
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37
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38 Converts feature records to BAM format.
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39
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40 .. class:: warningmark
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41
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42 BED files must be at least BED4 to create BAM (needs name field).
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43
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44 @REFERENCES@
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4
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45 ]]>
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46 </help>
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47 <expand macro="citations" />
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48 </tool>
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