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1 <tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="0.1.0">
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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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9 bedtools bedpetobam
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10 $ubam
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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 format="bed,gff,vcf" name="input" 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" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
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21 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
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22
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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" label="${input.name} (as BAM)"/>
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26 </outputs>
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27 <help>
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28
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29 **What it does**
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30
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31 Converts feature records to BAM format.
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32
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33 .. class:: warningmark
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34
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35 BED files must be at least BED4 to create BAM (needs name field).
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36
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37 @REFERENCES@
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38 </help>
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39 </tool>
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