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1 <tool id="preprocess" name="preprocess" version="0.0.1">
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2 <description>
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3 Preprocess Tumour Normal Pairs for Cancer Genomic Workflows
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.0.13">bamutil</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10
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11 ln -s $input_bam input.bam;
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12 ln -s $input_bam.metadata.bam_index input.bam.bai;
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13
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14 #if not $interval
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15 i="";
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16 #end if
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17
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18 {
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19 samtools view -H input.bam;
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20
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21 #if $interval
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22 for i in \$( cat $interval ); do
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23 #end if
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24
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25 samtools view -q $filter_qual input.bam \$i
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26
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27 #if $interval
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28 ; done
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29 #end if
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30 ;
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31 }
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32
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33 #if $clip_overlap
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34 | bam clipOverlap --in -.sam --out -.sam
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35 #end if
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36
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37 | samtools view -Sb - > $output;
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38
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39 ]]>
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40 </command>
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41 <inputs>
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42 <param type="data" format="bam" name="input_bam" label="Specify BAM Alignment File"/>
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43 <param type="data" format="bed,txt" name="interval" label="Specify Interval" optional="true"/>
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44 <param type="boolean" checked="true" name="clip_overlap" label="Clip Overlaps" help="Clips overlapping region between paired reads with lowest mean quality"/>
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45 <param type="integer" value="0" min="0" max="255" name="filter_qual" label="Minimum Mapping Quality" help="Filter reads with quality strictly less than MMQ"/>
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46 </inputs>
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47 <outputs>
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48 <data format="bam" name="output"/>
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49 </outputs>
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50 <stdio>
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51 <exit_code range="0" level="warning" description="Normal" />
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52 <exit_code range="1" level="fatal" description="Error in overclipping" />
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53 </stdio>
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54 </tool>
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