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1 <tool id="svdetect_preprocessing" name="BAM preprocessing">
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2
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3 <description>to get abnormal pairs</description>
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4
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5 <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name
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6 #if $newBam.pairNormal=="yes"
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7 -d -x '$normBAM'
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8 #end if
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9 '$inputBam'
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10 </command>
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11
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12 <inputs>
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13 <param name="sample_name" type="text" value="sample" label="Sample Name"/>
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14 <param name="inputBam" type="data" format="bam" label="BAM input file"/>
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15 <param name="readType" type="select" label="Read type">
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16 <option value="1">Illumina</option>
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17 <option value="0">SOLiD</option>
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18 </param>
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19 <param name="pairType" type="select" label="Library type">
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20 <option value="1">Paired-end</option>
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21 <option value="0">Mate-Pair</option>
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22 </param>
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23 <conditional name="newBam">
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24 <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam">
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25 <option value="no">No</option>
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26 <option value="yes">Yes</option>
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27 </param>
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28 <when value="yes">
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29 <!-- do nothing here -->
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30 </when>
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31 <when value="no">
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32 <!-- do nothing here -->
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33 </when>
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34 </conditional>
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35 <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/>
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36 <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/>
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37 <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/>
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38 <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/>
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39 </inputs>
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40
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41 <outputs>
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42 <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/>
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43 <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/>
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44 <data format="bam" name="normBAM" label="${$sample_name}.norm.bam">
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45 <filter>newBam['pairNormal'] == 'yes'</filter>
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46 </data>
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47 </outputs>
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48
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49 <help>
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50
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51 **What it does**
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52
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53 Bam_preprocessingPairs - Version 0.5
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54
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55 Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect.
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56
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57 From all pairs mapped onto the reference genome, this script outputs abnormal pairs:
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58
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59 * mapped on two different chromosomes
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60 * with an incorrect strand orientation and/or pair order
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61 * with an insert size distance +- sigma threshold
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62
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63 into a file prefix.ab.bam/sam sorted by read names
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64
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65 -BAM/SAM File input format only.
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66
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67 SAMtools required for BAM files
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68
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69 -----
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70
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71 .. class:: infomark
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72
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73 Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
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74
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75 </help>
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76
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77 </tool>
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