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1 <tool id="bedtools_multicovtbed" name="MultiCovBed" 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 #for $i, $bam in enumerate( $bams ):
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11 ln -s -f $bam ${i}.bam &&
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12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
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13 #end for
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4
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14
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15 bedtools multicov
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16 -bed $input
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17 -bams
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18 #for $i, $bam in enumerate( $bams ):
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19 ${i}.bam
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20 #end for
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21 $strand
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22 -f $overlap
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23 $reciprocal
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24 $split
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25 -q $q
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26 $duplicate
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27 $failed
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28 $proper
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29 > $output
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30 ]]>
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31 </command>
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32 <inputs>
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4
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33 <param name="input" format="bed" type="data" label="Sorted BED file" />
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34 <!-- Additional files, if the user needs more -->
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35 <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
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36
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37 <expand macro="strand2" />
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38 <expand macro="overlap" />
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39 <expand macro="reciprocal" />
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40 <expand macro="split" />
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41 <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
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42 <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
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43 label="Include duplicate reads"
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44 help="Default counts non-duplicates only. (-D)" />
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45 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
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46 label="Include failed-QC reads"
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47 help="Default counts pass-QC reads only (-F)"/>
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48 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
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49 label="Only count proper pairs"
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50 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
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51 </inputs>
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52 <outputs>
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4
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53 <data name="output" metadata_source="input" format_source="input" />
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54 </outputs>
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4
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55 <tests>
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56 <test>
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57 <param name="input" value="multiCov1.bed" ftype="bed" />
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58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
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59 <param name="q" value="1"/>
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60 <param name="split" value="False"/>
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61 <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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66 **What it does**
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67
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68 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
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69
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70
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71 @REFERENCES@
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4
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72 ]]>
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73 </help>
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1
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74 <expand macro="citations" />
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75 </tool>
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