# HG changeset patch # User nilesh # Date 1373562046 14400 # Node ID f2d331bf3d38dabfdf1d85380c327c6d290e1652 Uploaded diff -r 000000000000 -r f2d331bf3d38 bcftools_cat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_cat.xml Thu Jul 11 13:00:46 2013 -0400 @@ -0,0 +1,42 @@ + + This tool allows the user to concatenate BCF files. + + + samtools + + + bcftools cat $rinput > $output + + + + + + + + + + + + +**What it does:** + +This tool allows the user to concatenate BCF files. The input files are required to be sorted and have identical samples appearing in the same order. It does this using BCFtools cat from the SAMtools set of utilities: + +http://samtools.sourceforge.net/samtools.shtml#4 + +------ + +**Citation:** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__ + + .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html + +Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.) + + + + \ No newline at end of file diff -r 000000000000 -r f2d331bf3d38 bcftools_index.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_index.xml Thu Jul 11 13:00:46 2013 -0400 @@ -0,0 +1,40 @@ + + This tool allows the user to index sorted BCF for random access. + + + samtools + + + bcftools index $input > $output + + + + + + + + + + +**What it does:** + +This tool allows the user to index sorted BCF for random access using BCFtools index from the SAMtools set of utilities: + +http://samtools.sourceforge.net/samtools.shtml#4 + +------ + +**Citation:** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__ + + .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html + +Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.) + + + + \ No newline at end of file diff -r 000000000000 -r f2d331bf3d38 bcftools_view.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_view.xml Thu Jul 11 13:00:46 2013 -0400 @@ -0,0 +1,163 @@ + + Converts BCF format to VCF format + + samtools + + + bcftools view + #if str( $A ) == "true": + -A + #end if + #if str( $b ) == "true": + -b + #end if + #if $D.seq_dictionary == "true": + -D "$D.input" + #end if + #if str( $F ) == "true": + -F + #end if + #if str( $G ) == "true": + -G + #end if + #if str( $N ) == "true": + -N + #end if + #if str( $S ) == "true": + -S + #end if + #if str( $u) == "true": + -u + #end if + #if str( $c ) == "true": + -c + #end if + #if str( $e ) == "true": + -e + #end if + #if str( $g ) == "true": + -g + #end if + #if $i.alt_indel_snp_ratio == "true": + -i $i.ratio + #end if + #if $p.variant_filter == "true": + -p $p.float_value + #end if + #if $t.mutation_rate == "true": + -t $t.rate + #end if + #if str( $v ) == "true": + -v + #end if + $input + > $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does:** + +This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities: + +http://samtools.sourceforge.net/samtools.shtml#4 + +------ + +**Citation:** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__ + + .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html + +Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.) + + + diff -r 000000000000 -r f2d331bf3d38 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 11 13:00:46 2013 -0400 @@ -0,0 +1,23 @@ + + + + + + http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2 + make + + samtools + $INSTALL_DIR/bin + + + bcftools/bcftools + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + + + + Both BCFTools and Samtools installed in this dependency.Compiling SAMtools requires the ncurses and zlib development libraries. + +