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1 <tool id="bedtools_bamtobed" name="Convert from BAM to BED" 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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9 bedtools bamtobed
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10 $option
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11 $ed_score
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12 -i '$input'
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13 > '$output'
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14 #if str($tag):
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15 -tag $tag
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16 #end if
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17 </command>
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18 <inputs>
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19 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
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20 <param name="option" type="select" label="What type of BED output would you like">
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21 <option value="">Create a 6-column BED file.</option>
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22 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
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23 <option value="-bedpe">Create a paired-end, BEDPE format.</option>
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24 </param>
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25 <param name="split" type="boolean" label="Report each portion of a split BAM alignment" truevalue="-split" falsevalue="" checked="false" help="(i.e., having an 'N' CIGAR operation) as a distinct BED intervals."/>
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26 <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
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27 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
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28 </inputs>
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29 <outputs>
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30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
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31 </outputs>
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32 <help>
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33
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34 **What it does**
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35
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36 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
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37
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38 .. class:: infomark
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39
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40 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). This is important for RNA-seq and structural variation experiments.
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41
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42
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43 .. class:: warningmark
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44
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45 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
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46
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47 .. class:: warningmark
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48
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49 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
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50
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51 @REFERENCES@
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52
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53 </help>
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54 </tool>
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