Mercurial > repos > hepcat72 > extractsplitreads_bwamem

annotate extractSplitReads_BwaMem.xml @ 0:839c219ab0aa draft

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author hepcat72
date Fri, 10 Aug 2018 11:46:23 -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 <!-- Not sure yet how to call the command if the lumpy-sv package in bioconda doesn't put the script in an executable location on PATH -->
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12
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13 <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command>
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14
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15 <command detect_errors="aggressive">
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16 <![CDATA[
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17 extractSplitReads_BwaMem
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18 -i '$input'
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19 -n $numSplits
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20 $includeDups
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21 -m $minNonOverlap
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22 > '$output'
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23 ]]>
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24 </command>
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25
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26 <inputs>
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27
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28 <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/>
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29
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30 <param name="numSplits"
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31 label="numSplits"
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32 argument="--numSplits"
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33
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34 type="integer"
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35 value="2"
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36
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37 help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." />
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38
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39 <param name="includeDups"
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40 label="includeDups"
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41 argument="--includeDups"
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42
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43 type="boolean"
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44 truevalue="--includeDups"
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45 falsevalue=""
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46 checked="no"
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47 value="false"
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48
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49 help="Include alignments marked as duplicates." />
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50
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51 <param name="minNonOverlap"
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52 label="minNonOverlap"
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53 argument="--minNonOverlap"
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54
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55 type="integer"
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56 value="20"
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57
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58 help="Minimum non-overlap between split alignments on the query." />
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59
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60 </inputs>
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61 <outputs>
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62 <data format="sam" name="output" />
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63 </outputs>
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64
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65 <tests>
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66 <test>
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67 <param name="input" value="JS01-BWA-MEM.splitters.sam"/>
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68 <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/>
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69 </test>
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70 <test>
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71 <param name="input" value="pe.pos_sorted.sam"/>
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72 <output name="output" file="pe.pos_sorted.out.sam"/>
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73 </test>
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74 </tests>
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75
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76 <help>
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77 <![CDATA[
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78
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79 Usage: `extractSplitReads_BwaMem -i <file>`
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80
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81 extractSplitReads_BwaMem v0.1.0
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82
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83 Author: Ira Hall
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84
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85 Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates.
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86
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87 Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405.
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88
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89
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90 Options:
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91 -h, --help show this help message and exit
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92 -i FILE, --inFile=FILE
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93 A SAM file or standard input (-i stdin).
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94 -n INT, --numSplits=INT
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95 The maximum number of split-read mappings to allow per
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96 read. Reads with more are excluded. Default=2
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97 -d, --includeDups Include alignments marked as duplicates. Default=False
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98 -m INT, --minNonOverlap=INT
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99 minimum non-overlap between split alignments on the
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100 query (default=20)
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101
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102 ]]>
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103 </help>
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104
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105 <citations>
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106 <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation>
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107 </citations>
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108
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109 </tool>