Mercurial > repos > hepcat72 > extractsplitreads_bwamem
annotate extractSplitReads_BwaMem.xml @ 1:a20ac5d90c16 draft default tip
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author | hepcat72 |
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date | Fri, 10 Aug 2018 13:15:57 -0400 |
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1 <tool id="extractSplitReads_BwaMem" |
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2 name="Extract Split Reads" |
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3 version="0.1.0"> |
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4 |
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5 <description>from bwaMEM (part of lumpy-sv)</description> |
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6 |
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7 <requirements> |
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8 <requirement type="package" version="0.2.14a">lumpy-sv</requirement> |
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9 </requirements> |
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10 |
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11 <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command> |
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12 |
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13 <command detect_errors="aggressive"> |
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14 <![CDATA[ |
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15 extractSplitReads_BwaMem |
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16 -i '$input' |
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17 -n $numSplits |
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18 $includeDups |
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19 -m $minNonOverlap |
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20 > '$output' |
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21 ]]> |
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22 </command> |
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23 |
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24 <inputs> |
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25 |
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26 <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/> |
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27 |
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28 <param name="numSplits" |
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29 label="numSplits" |
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30 argument="--numSplits" |
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31 |
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32 type="integer" |
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33 value="2" |
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34 |
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35 help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." /> |
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36 |
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37 <param name="includeDups" |
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38 label="includeDups" |
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39 argument="--includeDups" |
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40 |
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41 type="boolean" |
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42 truevalue="--includeDups" |
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43 falsevalue="" |
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44 checked="no" |
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45 value="false" |
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46 |
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47 help="Include alignments marked as duplicates." /> |
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48 |
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49 <param name="minNonOverlap" |
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50 label="minNonOverlap" |
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51 argument="--minNonOverlap" |
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52 |
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53 type="integer" |
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54 value="20" |
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55 |
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56 help="Minimum non-overlap between split alignments on the query." /> |
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57 |
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58 </inputs> |
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59 <outputs> |
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60 <data format="sam" name="output" /> |
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61 </outputs> |
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62 |
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63 <tests> |
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64 <test> |
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65 <param name="input" value="JS01-BWA-MEM.splitters.sam"/> |
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66 <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/> |
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67 </test> |
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68 <test> |
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69 <param name="input" value="pe.pos_sorted.sam"/> |
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70 <output name="output" file="pe.pos_sorted.out.sam"/> |
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71 </test> |
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72 </tests> |
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73 |
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74 <help> |
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75 <![CDATA[ |
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76 |
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77 Usage: `extractSplitReads_BwaMem -i <file>` |
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78 |
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79 extractSplitReads_BwaMem v0.1.0 |
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80 |
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81 Author: Ira Hall |
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82 |
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83 Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates. |
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84 |
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85 Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405. |
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86 |
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87 |
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88 Options: |
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89 -h, --help show this help message and exit |
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90 -i FILE, --inFile=FILE |
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91 A SAM file or standard input (-i stdin). |
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92 -n INT, --numSplits=INT |
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93 The maximum number of split-read mappings to allow per |
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94 read. Reads with more are excluded. Default=2 |
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95 -d, --includeDups Include alignments marked as duplicates. Default=False |
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96 -m INT, --minNonOverlap=INT |
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97 minimum non-overlap between split alignments on the |
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98 query (default=20) |
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99 |
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100 ]]> |
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101 </help> |
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102 |
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103 <citations> |
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104 <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation> |
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105 </citations> |
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106 |
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107 </tool> |