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1 <tool id="cga_junctiondiff" name="junctiondiff(beta)" version="0.0.1">
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2
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3 <description>reports difference between junction calls</description> <!--adds description in toolbar-->
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4
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5 <requirements>
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6 <requirement type="binary">cgatools</requirement>
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7 </requirements>
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8
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9 <command> <!--run executable-->
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10 cgatools junctiondiff --beta -h
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11 </command>
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12
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13 <outputs>
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14 <data format="tabular" name="output" />
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15 </outputs>
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16
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17 <inputs>
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18 </inputs>
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19
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20 <help>
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21
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22 **What it does**
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23
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24 This tool reports difference between junction calls of Complete Genomics junctions files
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25
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26 cgatools: http://sourceforge.net/projects/cgatools/files/
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27
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28 -----
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29
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30 **cgatools Manual**::
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31
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32 COMMAND NAME
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33 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
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34
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35 DESCRIPTION
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36 junctiondiff takes two junction files A and B as input and produces the
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37 following output:
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38 - "diff-inputFileName" - the junctions from an input file A that are not
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39 present in input file B.
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40 - "report.txt" - a brief summary report (if --statout is used)
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41
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42 Two junctions are considered equivalent if:
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43 - they come from different files
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44 - left and right positions of one junction are not more than "--distance"
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45 bases apart from the corresponding positions of another junction
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46 - the junction scores are equal or above the scoreThreshold
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47 - they are on the same strands
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48
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49 OPTIONS
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50 -h [ --help ]
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51 Print this help message.
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52
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53 --beta
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54 This is a beta command. To run this command, you must pass the --beta
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55 flag.
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56
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57 -s [ --reference ] arg
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58 Reference file.
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59
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60 -a [ --junctionsA ] arg
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61 input junction file A.
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62
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63 -b [ --junctionsB ] arg
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64 input junction file B.
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65
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66 -A [ --scoreThresholdA ] arg (=10)
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67 score threshold value for the input file A.
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68
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69 -B [ --scoreThresholdB ] arg (=0)
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70 score threshold value for the input file B.
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71
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72 -d [ --distance ] arg (=200)
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73 Max distance between coordinates of potentially compatible junctions.
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74
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75 -l [ --minlength ] arg (=500)
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76 Minimum deletion junction length to be included into the difference
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77 file.
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78
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79 -o [ --output-prefix ] arg
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80 The path prefix for all the output reports.
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81
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82 -S [ --statout ]
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83 (Debug) Report various input file statistics. Experimental feature.
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84
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85 SUPPORTED FORMAT_VERSION
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86 1.5 or later
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87 </help>
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88 </tool>
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