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1 <tool id="samtools_bedcov" name="BedCov" version="2.0">
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2 <description>calculate read depth for a set of genomic intervals</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"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command><![CDATA[
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10 for bamfile in
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11 #for dataset in $input_bams:
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12 "${dataset}"
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13 #end for
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14 ; do
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15 if [ ! -f \$bamfile.bai ] ; then
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16 ln -s \$bamfile && samtools index `basename \$bamfile` ;
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17 else
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18 ln -s \$bamfile && ln -s \$bamfile.bai ;
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19 fi ;
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20 done ;
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21 samtools bedcov "${input_bed}"
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22 #for dataset in $input_bams:
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23 `basename "${dataset}"`
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24 #end for
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25 > "${output}"
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param name="input_bed" type="data" format="bed" label="BED file" />
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30 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
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31 </inputs>
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32 <outputs>
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33 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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38 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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39 <output name="output" file="samtools_bedcov_out1.tab" />
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40 </test>
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41 <test>
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42 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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43 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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44 <output name="output" file="samtools_bedcov_out2.tab" />
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45 </test>
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46 </tests>
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47 <help>
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48 **What it does**
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49
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50 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
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51
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52 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
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53
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54 </help>
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55 <expand macro="citations"></expand>
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56 </tool>
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57
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