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Commit message:
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/sam_stats commit 394834f8f34909961cfbf6252fefbdc63342d78d |
modified:
README.txt sam-stats.xml |
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diff -r b9e7569a4438 -r a51942c74761 README.txt --- a/README.txt Fri Jun 27 15:36:01 2014 -0400 +++ b/README.txt Mon Jul 13 11:45:51 2015 -0400 |
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@@ -1,12 +1,12 @@ -== sam-stats Galaxy Wrapper == +== ea-utils Galaxy Wrapper == -This is a Galaxy wrapper for the sam-stats tool from ea-utils suite. +This is a Galaxy wrapper for the sam-stats tools from the ea-utils suite. ** Installation ** Installation from a tool shed provides the necessary tool dependencies. -Otherwise, make sure sam-stats is in the path. +Otherwise, make sure fastq-join and sam-stats are 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. @@ -16,4 +16,3 @@ 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 b9e7569a4438 -r a51942c74761 sam-stats.xml --- a/sam-stats.xml Fri Jun 27 15:36:01 2014 -0400 +++ b/sam-stats.xml Mon Jul 13 11:45:51 2015 -0400 |
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@@ -1,9 +1,15 @@ -<tool id="sam_stats" name="sam-stats" version="1.32"> +<tool id="sam_stats" name="sam-stats" version="0.1"> <description> - Compute statistics from SAM or BAM files</description> + <requirements> <requirement type="package" version="1.1.2-484">ea-utils</requirement> </requirements> - <command> + + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error occurred" /> + </stdio> + + <command><![CDATA[ sam-stats $trackMultAlign $reportAllChr @@ -15,10 +21,12 @@ #end if -S $histBinSize $input - > $samStats + > $samStats + ]]> </command> + <inputs> - <param format="sam,bam" name="input" type="data" label="SAM/BAM File" /> + <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)" /> --> @@ -32,10 +40,6 @@ </data> </outputs> - <stdio> - <exit_code range="1:" level="fatal" description="Unknown error occurred" /> - </stdio> - <tests> <test> <param name="input" value="test.sam" /> @@ -43,14 +47,14 @@ </test> </tests> - <help> + <help><![CDATA[ Overview -------- sam-stats computes varius statics on SAM/BAM alignment files. Complete Stats:: - <STATS> : mean, max, stdev, median, Q1 (25 percentile), Q3 + <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 @@ -62,14 +66,14 @@ 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 + 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 + base qual <STATS> : stats for base qualities A,T,C,G : base percentages Meaning of the per-chromosome signature: @@ -79,5 +83,27 @@ 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> + + <citations> + <citation type="bibtex"> + @article{aronesty_comparison_2013, + title = {Comparison of {Sequencing} {Utility} {Programs}}, + volume = {7}, + issn = {18750362}, + url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1}, + doi = {10.2174/1875036201307010001}, + language = {en}, + number = {1}, + urldate = {2015-07-10}, + journal = {The Open Bioinformatics Journal}, + author = {Aronesty, Erik}, + month = jan, + year = {2013}, + pages = {1--8} + } + </citation> + </citations> + </tool> |