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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:35:52 -0400
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da985dad64c0 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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1 <tool id="sam_stats" name="sam-stats" version="1.38.763">
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2 <description> - Compute statistics from SAM or BAM files</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.1.2-806">ea-utils</requirement>
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6 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
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10 </stdio>
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12 <command><![CDATA[
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13 sam-stats
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14 $trackMultAlign
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15 $reportAllChr
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16 #if $rnaSeqStats:
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17 -R $rnaSeqStatsFile
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18 #end if
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19 #if $input.extension == "bam":
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20 -B
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21 #end if
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22 -S $histBinSize
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23 $input
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24 > $samStats
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25 ]]>
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26 </command>
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27
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28 <inputs>
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29 <param format="sam, bam" name="input" type="data" label="SAM/BAM File" />
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30 <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" />
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31 <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" />
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32 <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> -->
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33 <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome &quot;histogram&quot;" />
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34 <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" />
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35 </inputs>
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36
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37 <outputs>
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38 <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/>
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39 <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter>
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40 </data>
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="input" value="test.sam" />
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46 <output name="samStats" file="testout.txt" />
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47 </test>
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48 </tests>
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49
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50 <help><![CDATA[
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51 Overview
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52 --------
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53 sam-stats computes varius statics on SAM/BAM alignment files.
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54
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55 Complete Stats::
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56
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57 <STATS> : mean, max, stdev, median, Q1 (25 percentile), Q3
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58 reads : # of entries in the sam file, might not be # reads
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59 phred : phred scale used
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60 bsize : # reads used for qual stats
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61 mapped reads : number of aligned reads (unique probe id sequences)
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62 mapped bases : total of the lengths of the aligned reads
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63 forward : number of forward-aligned reads
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64 reverse : number of reverse-aligned reads
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65 snp rate : mismatched bases / total bases
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66 ins rate : insert bases / total bases
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67 del rate : deleted bases / total bases
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68 pct mismatch : percent of reads that have mismatches
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69 len <STATS> : read length stats, ignored if fixed-length
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70 mapq <STATS> : stats for mapping qualities
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71 insert <STATS> : stats for insert sizes
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72 <CHR> : percentage of mapped bases per chr, followed by a signature
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73
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74 Subsampled stats (1M reads max)::
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75
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76 base qual <STATS> : stats for base qualities
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77 A,T,C,G : base percentages
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78
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79 Meaning of the per-chromosome signature:
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80
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81 A ascii-histogram of mapped reads by chromosome position. It is only output if the original SAM/BAM has a header. The values are the log2 of the # of mapped reads at each position + ascii '0'.
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82
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83 See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means.
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84
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85 This tool uses the sam-stats program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/SamStats for details.
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86 ]]>
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87 </help>
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88
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89 <citations>
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90 <citation type="bibtex">
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91 @article{aronesty_comparison_2013,
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92 title = {Comparison of {Sequencing} {Utility} {Programs}},
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93 volume = {7},
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94 issn = {18750362},
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95 url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
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96 doi = {10.2174/1875036201307010001},
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97 language = {en},
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98 number = {1},
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99 urldate = {2015-07-10},
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100 journal = {The Open Bioinformatics Journal},
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101 author = {Aronesty, Erik},
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102 month = jan,
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103 year = {2013},
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104 pages = {1--8}
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105 }
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106 </citation>
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107 </citations>
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108
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109 </tool>