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comparison sam-stats.xml @ 1:a51942c74761 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d
author lparsons
date Mon, 13 Jul 2015 11:45:51 -0400
parents b9e7569a4438
children da985dad64c0
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0:b9e7569a4438 1:a51942c74761
1 <tool id="sam_stats" name="sam-stats" version="1.32"> 1 <tool id="sam_stats" name="sam-stats" version="0.1">
2 <description> - Compute statistics from SAM or BAM files</description> 2 <description> - Compute statistics from SAM or BAM files</description>
3
3 <requirements> 4 <requirements>
4 <requirement type="package" version="1.1.2-484">ea-utils</requirement> 5 <requirement type="package" version="1.1.2-484">ea-utils</requirement>
5 </requirements> 6 </requirements>
6 <command> 7
8 <stdio>
9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
10 </stdio>
11
12 <command><![CDATA[
7 sam-stats 13 sam-stats
8 $trackMultAlign 14 $trackMultAlign
9 $reportAllChr 15 $reportAllChr
10 #if $rnaSeqStats: 16 #if $rnaSeqStats:
11 -R $rnaSeqStatsFile 17 -R $rnaSeqStatsFile
13 #if $input.extension == "bam": 19 #if $input.extension == "bam":
14 -B 20 -B
15 #end if 21 #end if
16 -S $histBinSize 22 -S $histBinSize
17 $input 23 $input
18 &gt; $samStats 24 > $samStats
25 ]]>
19 </command> 26 </command>
27
20 <inputs> 28 <inputs>
21 <param format="sam,bam" name="input" type="data" label="SAM/BAM File" /> 29 <param format="sam, bam" name="input" type="data" label="SAM/BAM File" />
22 <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" /> 30 <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" />
23 <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" /> 31 <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" />
24 <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> --> 32 <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> -->
25 <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome &quot;histogram&quot;" /> 33 <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome &quot;histogram&quot;" />
26 <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" /> 34 <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" />
30 <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/> 38 <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/>
31 <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter> 39 <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter>
32 </data> 40 </data>
33 </outputs> 41 </outputs>
34 42
35 <stdio>
36 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
37 </stdio>
38
39 <tests> 43 <tests>
40 <test> 44 <test>
41 <param name="input" value="test.sam" /> 45 <param name="input" value="test.sam" />
42 <output name="samStats" file="testout.txt" /> 46 <output name="samStats" file="testout.txt" />
43 </test> 47 </test>
44 </tests> 48 </tests>
45 49
46 <help> 50 <help><![CDATA[
47 Overview 51 Overview
48 -------- 52 --------
49 sam-stats computes varius statics on SAM/BAM alignment files. 53 sam-stats computes varius statics on SAM/BAM alignment files.
50 54
51 Complete Stats:: 55 Complete Stats::
52 56
53 &lt;STATS&gt; : mean, max, stdev, median, Q1 (25 percentile), Q3 57 <STATS> : mean, max, stdev, median, Q1 (25 percentile), Q3
54 reads : # of entries in the sam file, might not be # reads 58 reads : # of entries in the sam file, might not be # reads
55 phred : phred scale used 59 phred : phred scale used
56 bsize : # reads used for qual stats 60 bsize : # reads used for qual stats
57 mapped reads : number of aligned reads (unique probe id sequences) 61 mapped reads : number of aligned reads (unique probe id sequences)
58 mapped bases : total of the lengths of the aligned reads 62 mapped bases : total of the lengths of the aligned reads
60 reverse : number of reverse-aligned reads 64 reverse : number of reverse-aligned reads
61 snp rate : mismatched bases / total bases 65 snp rate : mismatched bases / total bases
62 ins rate : insert bases / total bases 66 ins rate : insert bases / total bases
63 del rate : deleted bases / total bases 67 del rate : deleted bases / total bases
64 pct mismatch : percent of reads that have mismatches 68 pct mismatch : percent of reads that have mismatches
65 len &lt;STATS&gt; : read length stats, ignored if fixed-length 69 len <STATS> : read length stats, ignored if fixed-length
66 mapq &lt;STATS&gt; : stats for mapping qualities 70 mapq <STATS> : stats for mapping qualities
67 insert &lt;STATS&gt; : stats for insert sizes 71 insert <STATS> : stats for insert sizes
68 &lt;CHR&gt; : percentage of mapped bases per chr, followed by a signature 72 <CHR> : percentage of mapped bases per chr, followed by a signature
69 73
70 Subsampled stats (1M reads max):: 74 Subsampled stats (1M reads max)::
71 75
72 base qual &lt;STATS&gt; : stats for base qualities 76 base qual <STATS> : stats for base qualities
73 A,T,C,G : base percentages 77 A,T,C,G : base percentages
74 78
75 Meaning of the per-chromosome signature: 79 Meaning of the per-chromosome signature:
76 80
77 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'. 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'.
78 82
79 See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means. 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.
80 84
81 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. 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.
86 ]]>
82 </help> 87 </help>
88
89 <citations>
90 <citation type="bibtex">
91 @article{aronesty_comparison_2013,
92 title = {Comparison of {Sequencing} {Utility} {Programs}},
93 volume = {7},
94 issn = {18750362},
95 url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
96 doi = {10.2174/1875036201307010001},
97 language = {en},
98 number = {1},
99 urldate = {2015-07-10},
100 journal = {The Open Bioinformatics Journal},
101 author = {Aronesty, Erik},
102 month = jan,
103 year = {2013},
104 pages = {1--8}
105 }
106 </citation>
107 </citations>
108
83 </tool> 109 </tool>