Mercurial > repos > devteam > samtools_flagstat
changeset 2:728e2ed819a1 draft
Uploaded tool version 1.0.2, updated for samtools 1.0.
| author | devteam |
|---|---|
| date | Wed, 24 Sep 2014 11:26:48 -0400 |
| parents | f92f13ccee76 |
| children | 480404be9626 |
| files | samtools_flagstat.xml test-data/samtools_flagstat_out1.txt tool_dependencies.xml |
| diffstat | 3 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- 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 @@ -<tool id="samtools_flagstat" name="flagstat" version="1.0.1"> +<tool id="samtools_flagstat" name="flagstat" version="1.0.2"> <requirements> - <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.0">samtools</requirement> </requirements> <description>provides simple stats on BAM files</description> <command>samtools flagstat "$input1" > "$output1" @@ -34,4 +34,4 @@ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> -</tool> +</tool> \ No newline at end of file
--- 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)
--- 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 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.0"> + <repository changeset_revision="da217d52e81c" name="package_samtools_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>