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1 <tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4">
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2 <description></description>
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3
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4 <requirements>
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5 <requirement type="binary">bamToBed</requirement>
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6 </requirements>
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7
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8 <command>
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9 bamToBed $option $ed_score -i '$input' > '$output'
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10 #if str($tag):
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11 -tag $tag
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12 #end if
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13 </command>
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14
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15 <inputs>
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16 <param format="bam" name="input" type="data" label="Input BAM file"/>
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17 <param name="option" type="select" label="Output formatting options">
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18 <option value="">Create a 6-column BED file.</option>
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19 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
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20 <option value="-bedpe">Create a paired-end, BEDPE format.</option>
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21 </param>
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22 <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/>
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23 <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
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24 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
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25 </inputs>
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26
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27 <outputs>
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28 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
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29 </outputs>
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30
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31 <help>
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32
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33 **What it does**
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34
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35 This tool converts a BAM file to a BED file. The end coordinate is computed
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36 by inspecting the CIGAR string. The QNAME for the alignment is used as the
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37 BED name field and, by default, the MAPQ is used as the BED score.
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38
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39 ------
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40
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41
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42 This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.
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43
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44 .. __: http://code.google.com/p/bedtools/
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45 .. __: http://cphg.virginia.edu/quinlan/
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46
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47 </help>
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48 </tool>
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