1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/55f8f2d8ac18/ changeset: 55f8f2d8ac18 user: dan date: 2011-08-31 22:50:58 summary: Add samtools rmdup tool. affected #: 4 files (105 bytes) --- a/tool_conf.xml.main Wed Aug 31 11:44:52 2011 -0400 +++ b/tool_conf.xml.main Wed Aug 31 16:50:58 2011 -0400 @@ -382,6 +382,7 @@ <tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" /> + <tool file="samtools/samtools_rmdup.xml" /></section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /> --- a/tool_conf.xml.sample Wed Aug 31 11:44:52 2011 -0400 +++ b/tool_conf.xml.sample Wed Aug 31 16:50:58 2011 -0400 @@ -352,8 +352,9 @@ <tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /><tool file="samtools/samtools_flagstat.xml" /> + <tool file="samtools/samtools_rmdup.xml" /></section> - <section name="NGS: GATK Tools" id="gatk"> + <section name="NGS: GATK Tools (beta)" id="gatk"><label text="Realignment" id="gatk_realignment" /><tool file="gatk/realigner_target_creator.xml" /><tool file="gatk/indel_realigner.xml" /> --- a/tools/samtools/samtools_flagstat.xml Wed Aug 31 11:44:52 2011 -0400 +++ b/tools/samtools/samtools_flagstat.xml Wed Aug 31 16:50:58 2011 -0400 @@ -3,7 +3,7 @@ <requirement type="package">samtools</requirement></requirements><description>provides simple stats on BAM files</description> - <command>samtools flagstat $input1 > $output1 + <command>samtools flagstat "$input1" > "$output1" </command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.