Mercurial > repos > hepcat72 > extractsplitreads_bwamem

annotate extractSplitReads_BwaMem.xml @ 1:a20ac5d90c16 draft default tip

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author hepcat72
date Fri, 10 Aug 2018 13:15:57 -0400
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1 <tool id="extractSplitReads_BwaMem"
0
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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>