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20
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1 <tool id="svdetect_import" name="Import data">
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2 <description>BAM, chromosome info or sv files</description>
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3 <command interpreter="bash">SVDetect_import.sh -i $file_path
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4 #if str($type.file_type)=="bam"
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5 -o $outbamfile
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6 #elif str($type.file_type)=="len"
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7 -o $outlenfile
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8 #elif str($type.file_type)=="sv"
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9 -o $outsvfile
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10 #end if
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11 </command>
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12 <inputs>
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13 <param name="file_name" type="text" value="file1" label="File Name"/>
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14 <conditional name="type">
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15 <param name="file_type" type="select" label="Select the file type to import" help="BAM file (BAM) or text file (SAM, chromosome list or a SV tabulated text file)">
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16 <option value="bam">BAM file (.bam)</option>
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17 <option value="len">Chromosome info file (.len)</option>
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18 <option value="sv">SVDetect output file (.sv)</option>
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19 </param>
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20 <when value="bam">
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21 <!-- do nothing here -->
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22 </when>
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23 <when value="len">
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24 <!-- do nothing here -->
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25 </when>
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26 <when value="sv">
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27 <!-- do nothing here -->
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28 </when>
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29 </conditional>
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30 <param name="file_path" type="text" size="150" label="Path to file"/>
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31 </inputs>
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32 <outputs>
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33 <data format="bam" name="outbamfile" label="${file_name}.bam">
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34 <filter>type['file_type']=="bam"</filter>
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35 </data>
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36 <data format="len" name="outlenfile" label="${file_name}.len">
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37 <filter>type['file_type']=="len"</filter>
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38 </data>
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39 <data format="sv" name="outsvfile" label="${file_name}.sv">
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40 <filter>type['file_type']=="sv"</filter>
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41 </data>
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42 </outputs>
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43 <help>
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44 **What it does**
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45
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46 This tool allows you to import quickly a BAM file, a chromosome info file or a SVDetect output file from you computer as inputs for SVDetect.
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47
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48
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49 **Example of chromosome file**
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50
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51 Input len file::
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52
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53 1 chr1 247249719
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54 2 chr2 242951149
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55 3 chr3 199501827
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56 4 chr4 191273063
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57 5 chr5 180857866
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58 6 chr6 170899992
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59 7 chr7 158821424
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60 8 chr8 146274826
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61 9 chr9 140273252
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62 10 chr10 135374737
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63 11 chr11 134452384
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64 12 chr12 132349534
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65 13 chr13 114142980
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66 14 chr14 106368585
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67 15 chr15 100338915
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68 16 chr16 88827254
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69 17 chr17 78774742
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70 18 chr18 76117153
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71 19 chr19 63811651
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72 20 chr20 62435964
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73 21 chr21 46944323
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74 22 chr22 49691432
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75 23 chrX 154913754
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76 24 chrY 57772954
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77
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78 -----
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79
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80 .. class:: infomark
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81
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82 Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
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83 </help>
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84
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85 </tool>
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