Mercurial > repos > lparsons > sam_stats
annotate sam-stats.xml @ 1:a51942c74761 draft
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
author | lparsons |
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date | Mon, 13 Jul 2015 11:45:51 -0400 |
parents | b9e7569a4438 |
children | da985dad64c0 |
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a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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1 <tool id="sam_stats" name="sam-stats" version="0.1"> |
0 | 2 <description> - Compute statistics from SAM or BAM files</description> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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3 |
0 | 4 <requirements> |
5 <requirement type="package" version="1.1.2-484">ea-utils</requirement> | |
6 </requirements> | |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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7 |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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8 <stdio> |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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9 <exit_code range="1:" level="fatal" description="Unknown error occurred" /> |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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10 </stdio> |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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11 |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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12 <command><![CDATA[ |
0 | 13 sam-stats |
14 $trackMultAlign | |
15 $reportAllChr | |
16 #if $rnaSeqStats: | |
17 -R $rnaSeqStatsFile | |
18 #end if | |
19 #if $input.extension == "bam": | |
20 -B | |
21 #end if | |
22 -S $histBinSize | |
23 $input | |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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24 > $samStats |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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25 ]]> |
0 | 26 </command> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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27 |
0 | 28 <inputs> |
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a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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29 <param format="sam, bam" name="input" type="data" label="SAM/BAM File" /> |
0 | 30 <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" /> |
31 <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" /> | |
32 <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> --> | |
33 <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome "histogram"" /> | |
34 <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" /> | |
35 </inputs> | |
36 | |
37 <outputs> | |
38 <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/> | |
39 <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter> | |
40 </data> | |
41 </outputs> | |
42 | |
43 <tests> | |
44 <test> | |
45 <param name="input" value="test.sam" /> | |
46 <output name="samStats" file="testout.txt" /> | |
47 </test> | |
48 </tests> | |
49 | |
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a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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50 <help><![CDATA[ |
0 | 51 Overview |
52 -------- | |
53 sam-stats computes varius statics on SAM/BAM alignment files. | |
54 | |
55 Complete Stats:: | |
56 | |
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a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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57 <STATS> : mean, max, stdev, median, Q1 (25 percentile), Q3 |
0 | 58 reads : # of entries in the sam file, might not be # reads |
59 phred : phred scale used | |
60 bsize : # reads used for qual stats | |
61 mapped reads : number of aligned reads (unique probe id sequences) | |
62 mapped bases : total of the lengths of the aligned reads | |
63 forward : number of forward-aligned reads | |
64 reverse : number of reverse-aligned reads | |
65 snp rate : mismatched bases / total bases | |
66 ins rate : insert bases / total bases | |
67 del rate : deleted bases / total bases | |
68 pct mismatch : percent of reads that have mismatches | |
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a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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69 len <STATS> : read length stats, ignored if fixed-length |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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70 mapq <STATS> : stats for mapping qualities |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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71 insert <STATS> : stats for insert sizes |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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72 <CHR> : percentage of mapped bases per chr, followed by a signature |
0 | 73 |
74 Subsampled stats (1M reads max):: | |
75 | |
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a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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76 base qual <STATS> : stats for base qualities |
0 | 77 A,T,C,G : base percentages |
78 | |
79 Meaning of the per-chromosome signature: | |
80 | |
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'. | |
82 | |
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. | |
84 | |
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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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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86 ]]> |
0 | 87 </help> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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88 |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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89 <citations> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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90 <citation type="bibtex"> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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91 @article{aronesty_comparison_2013, |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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92 title = {Comparison of {Sequencing} {Utility} {Programs}}, |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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93 volume = {7}, |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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94 issn = {18750362}, |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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95 url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1}, |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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96 doi = {10.2174/1875036201307010001}, |
a51942c74761
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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97 language = {en}, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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98 number = {1}, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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99 urldate = {2015-07-10}, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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100 journal = {The Open Bioinformatics Journal}, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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101 author = {Aronesty, Erik}, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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102 month = jan, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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103 year = {2013}, |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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104 pages = {1--8} |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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105 } |
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106 </citation> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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107 </citations> |
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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
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108 |
0 | 109 </tool> |