# HG changeset patch # User devteam # Date 1411572408 14400 # Node ID 728e2ed819a1452b47c1611ce44d946bc6f2096a # Parent f92f13ccee76270399632dc7db86b509f6c6507d Uploaded tool version 1.0.2, updated for samtools 1.0. diff -r f92f13ccee76 -r 728e2ed819a1 samtools_flagstat.xml --- a/samtools_flagstat.xml Thu Mar 27 14:05:16 2014 -0400 +++ b/samtools_flagstat.xml Wed Sep 24 11:26:48 2014 -0400 @@ -1,6 +1,6 @@ - + - samtools + samtools provides simple stats on BAM files samtools flagstat "$input1" > "$output1" @@ -34,4 +34,4 @@ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - + \ No newline at end of file diff -r f92f13ccee76 -r 728e2ed819a1 test-data/samtools_flagstat_out1.txt --- a/test-data/samtools_flagstat_out1.txt Thu Mar 27 14:05:16 2014 -0400 +++ b/test-data/samtools_flagstat_out1.txt Wed Sep 24 11:26:48 2014 -0400 @@ -1,11 +1,11 @@ 10 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates -10 + 0 mapped (100.00%:nan%) +10 + 0 mapped (100.00%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 -0 + 0 properly paired (nan%:nan%) +0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped -0 + 0 singletons (nan%:nan%) +0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) diff -r f92f13ccee76 -r 728e2ed819a1 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 27 14:05:16 2014 -0400 +++ b/tool_dependencies.xml Wed Sep 24 11:26:48 2014 -0400 @@ -1,6 +1,6 @@ - - + +