| Next changeset 1:a51942c74761 (2015-07-13) |
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Commit message:
Uploaded initial version with package dependency. |
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added:
README.txt sam-stats.xml test-data/test.sam test-data/testout.txt tool_dependencies.xml |
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| diff -r 000000000000 -r b9e7569a4438 README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Fri Jun 27 15:36:01 2014 -0400 |
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| @@ -0,0 +1,19 @@ +== sam-stats Galaxy Wrapper == + +This is a Galaxy wrapper for the sam-stats tool from ea-utils suite. + +** Installation ** + +Installation from a tool shed provides the necessary tool dependencies. + +Otherwise, make sure sam-stats is in the path. +Move the test data files to your galaxy root test-data. +Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them. +Restart the Galaxy server. + +** Attribution ** + +The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/ + +The galaxy wrapper code was written by Lance Parsons (lparsons@princeton.edu), Lewis-Sigler Institute for Integrative Genomics, Princeton University. +The code is housed on BitBucket at: https://bitbucket.org/lance_parsons/ea_utils_galaxy_wrapper |
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| diff -r 000000000000 -r b9e7569a4438 sam-stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam-stats.xml Fri Jun 27 15:36:01 2014 -0400 |
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| @@ -0,0 +1,83 @@ +<tool id="sam_stats" name="sam-stats" version="1.32"> + <description> - Compute statistics from SAM or BAM files</description> + <requirements> + <requirement type="package" version="1.1.2-484">ea-utils</requirement> + </requirements> + <command> + sam-stats + $trackMultAlign + $reportAllChr + #if $rnaSeqStats: + -R $rnaSeqStatsFile + #end if + #if $input.extension == "bam": + -B + #end if + -S $histBinSize + $input + > $samStats + </command> + <inputs> + <param format="sam,bam" name="input" type="data" label="SAM/BAM File" /> + <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" /> + <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" /> + <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> --> + <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome "histogram"" /> + <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" /> + </inputs> + + <outputs> + <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/> + <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter> + </data> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error occurred" /> + </stdio> + + <tests> + <test> + <param name="input" value="test.sam" /> + <output name="samStats" file="testout.txt" /> + </test> + </tests> + + <help> +Overview +-------- +sam-stats computes varius statics on SAM/BAM alignment files. + +Complete Stats:: + + <STATS> : mean, max, stdev, median, Q1 (25 percentile), Q3 + reads : # of entries in the sam file, might not be # reads + phred : phred scale used + bsize : # reads used for qual stats + mapped reads : number of aligned reads (unique probe id sequences) + mapped bases : total of the lengths of the aligned reads + forward : number of forward-aligned reads + reverse : number of reverse-aligned reads + snp rate : mismatched bases / total bases + ins rate : insert bases / total bases + del rate : deleted bases / total bases + pct mismatch : percent of reads that have mismatches + len <STATS> : read length stats, ignored if fixed-length + mapq <STATS> : stats for mapping qualities + insert <STATS> : stats for insert sizes + <CHR> : percentage of mapped bases per chr, followed by a signature + +Subsampled stats (1M reads max):: + + base qual <STATS> : stats for base qualities + A,T,C,G : base percentages + +Meaning of the per-chromosome signature: + + 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'. + +See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means. + +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. + </help> +</tool> |
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| diff -r 000000000000 -r b9e7569a4438 test-data/test.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Fri Jun 27 15:36:01 2014 -0400 |
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| b'@@ -0,0 +1,100 @@\n+GEN-SEQ-ANA_0001:1:1:17434:14109#0/1\t0\tPCRPRIMER1\t5\t255\t33M\t*\t0\t0\tATACGGCGACCACCGAGATCTACACTCTTTCCC\t?<??>>BB>>A5AAA;;9:B<A?:AAA<B<AAA\tXA:i:0\tMD:Z:33\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:4183:5576#0/1\t0\tPCRPRIMER1+1\t1\t255\t38M\t*\t0\t0\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCT\tAA=A=7=>;<BB8;>5>>?:B>BAABBBBBBBBABBB;\tXA:i:0\tMD:Z:38\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:16837:9043#0/1\t0\tPCRPRIMER1+1\t14\t255\t27M\t*\t0\t0\tCCACCGAGATCTACACTCTTTCCCTAC\t?BB?ABB?BBB<7A5?7??A?<AA?A?\tXA:i:0\tMD:Z:27\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:6753:19078#0/1\t0\tPCRPRIMER1+1\t58\t255\t25M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATC\tA:BABA:AA<?B<<?BBBBBB@BBB\tXA:i:0\tMD:Z:25\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:14641:6640#0/1\t0\tPCRPRIMER1+1\t58\t255\t43M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACAC\tAC@CB>:CC>CCCCCC?@CCBB<?@B@BAB@ABBBBBB5:?5?\tXA:i:0\tMD:Z:43\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:18498:19719#0/1\t0\tPCRPRIMER1+1\t58\t255\t38M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCC\tCCCCCCCCCBCCACCC@CCC@BCCCCCC@CCCCCCCCC\tXA:i:0\tMD:Z:38\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:5165:8271#0/1\t0\tPCRPRIMER1+2\t1\t255\t37M\t*\t0\t0\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCC\tCC=CC>CC:@CCC@C>BAB<B>AAA88?>>ABBB:AA\tXA:i:0\tMD:Z:37\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:3890:20139#0/1\t0\tPCRPRIMER2+1\t34\t255\t23M\t*\t0\t0\tTAATGATACGGCGACCACCGAGA\tCCCCCC<CBB;;C@CC5<CABB7\tXA:i:0\tMD:Z:23\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:6236:11228#0/1\t0\tPCRPRIMER2+1\t34\t255\t20M\t*\t0\t0\tTAATGATACGGCGACCACCG\tCCCCCC8CCCCC=CC?AAAA\tXA:i:0\tMD:Z:20\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:13390:7511#0/1\t0\tPCRPRIMER2+1\t34\t255\t48M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC\tCCACBCBBBCCCCCCC?CCC;C?CCC?CCCCCCCCCCCACCCC;=>8A\tXA:i:0\tMD:Z:48\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:16810:9063#0/1\t0\tPCRPRIMER2+1\t34\t255\t45M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA\tCCCCCCCCBCCCBBCCCCCCCCCCCCCCBA=@CCCCBC5B@9@@@\tXA:i:0\tMD:Z:45\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:1127:14386#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTGAATTCATGAATGGAAAAA\t?ACC<@>69@6>@BB?@:==\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1210:17845#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCAAAATCTTGCCGAT\t>===>>@@@=<89A<B:@:BAA@@\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1260:17853#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCAGGACCACGCGTAAACGTCACC\tCCCCCB;ACBBB6@BB@BBB=A?A>6>AB?>B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1227:4069#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTCGAGAATTCTTTATCAACCTCGTT\t=CCCCCBC6@BCCC=9BA7A>>BB>\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1309:16895#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCCCTCATTCTTGGATTTGTA\tCA>CC@BBC8C@C>=C5<CCC@?CC;?>;\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1290:1939#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTACGTAATTCCGTGTCGGAGCCCGT\t??B:6>B;>AB=>B>B:BB>?A<6?\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1311:12611#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAATTCGTTTATTTTTGTATTT\tBBBBB@@@@@@@B:====:BBA\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1312:13847#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAAATTCCTTGCTTCAACGATGCA\t?BB>=8CC@??CCCC@B?>CC:CCC:8\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1327:14127#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATAAATTCAGAATAGTTTCACT\t=A:??B>=;B@A;97C>B@=6B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1328:16612#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCTTCTCATCGG\t@@@8@;C@C@CC=BC=>=AA\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1339:13574#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTTCTGTGATAATTTCAATATTGCC\tCB8B>=B=ABBBB:=BABBB@>=6\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1343:12008#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTTCGGCACTTTTCAGCACAATTTTCA\tCA=ACC@CC@BB=?AC??CC?CC?<C\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1353:17775#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAACTTCCCAACAGTGTTGTAAAG\t>5CBC?8?C=?ACBC>CCBB@=CAA8:\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1358:3384#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAACAAACCATGTTTTGCCCTCAAACAG\tB8:BBBBB:BBB=BBBA@<BBB>BB:9\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1361:15054#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATGCTAATTCAGTAGCTATTGTTCTCCAAAT\tBCC:?CA?C?=CC?ABC@<?B@C@CC@8C>C\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1362:13972#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTAATTCTTCGCGAGTCTTTG\t@>C?CA?:@??@@@@CC?C?B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1363:2154#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAGCTGAATTCTAGAAATGAAGAATATTTTTATTTATTTTCAG\tCB@C?B;CC=CAAC@@>:C?@:???CCBB>8>>>>?C>6>A?\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1373:2799#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCAAAACTACTACTGTAGAGGGGTACTG\t?BABACCCC@B=<=@@?8B><@B@>BAAB9<@<>@B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1374:3530#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCTTCCTCCTTAA\tAAAC8A=CA>CC@CC:B7ACC\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1379:7364#0/1'..b'CCC?\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1475:14575#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTACGTAATTCGAAATTTGAG\t?CB@C==AA?C=CCCBB:@B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1480:6616#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCGAGCGCAAAGG\tC;CCCCCCC?C@C9CC?CCC:\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1481:5435#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTATGAATAGAGAACTTTTA\tB@B6BBB=B>@@=@=@@BBBB>B?>B=\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1481:5276#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCGAATGAAATCATA\tCCCCBBCDB@C=CDACCC=C?C>\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1482:10064#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAAATTCAATTTGAAAA\tCC=CCC6C@;CCCBCAB?9B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:148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| diff -r 000000000000 -r b9e7569a4438 test-data/testout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.txt Fri Jun 27 15:36:01 2014 -0400 |
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| @@ -0,0 +1,29 @@ +reads 100 +version 1.32 +mapped reads 11 +mapped bases 377 +phred 33 +forward 0 +reverse 11 +len max 48 +len mean 34.2727 +len stdev 9.4137 +mapq mean 255.0000 +mapq stdev 0.0000 +mapq Q1 255.00 +mapq median 255.00 +mapq Q3 255.00 +snp rate 0.000000 +pct mismatch 0.0000 +base qual mean 31.5650 +base qual stdev 3.2627 +%A 27.5862 +%C 34.4828 +%G 16.7109 +%T 21.2202 +%PCRPRIMER1 8.753316 +%PCRPRIMER1+1 45.358090 +%PCRPRIMER1+2 9.814324 +%PCRPRIMER2+1 36.074271 +num ref seqs 4 +num ref aligned 4 |
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| diff -r 000000000000 -r b9e7569a4438 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 27 15:36:01 2014 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ea-utils" version="1.1.2-484"> + <repository changeset_revision="ef9389074f0a" name="package_ea_utils_1_1_2_484" owner="lparsons" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |