Mercurial > repos > nilesh > bcftools
changeset 0:f2d331bf3d38
Uploaded
| author | nilesh |
|---|---|
| date | Thu, 11 Jul 2013 13:00:46 -0400 |
| parents | |
| children | 3182c7fac413 |
| files | bcftools_cat.xml bcftools_index.xml bcftools_view.xml tool_dependencies.xml |
| diffstat | 4 files changed, 268 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<tool id="BCF Tools Cat" name="BCF Tools Cat"> + <description>This tool allows the user to concatenate BCF files.</description> + + <requirements> + <requirements type="package">samtools</requirements> + </requirements> + + <command interpreter="python">bcftools cat $rinput > $output </command> + + <inputs> + <repeat name="rinput" title="BCF File"> + <param name="input" type="data" format="bcf" label="File"/> + </repeat> + </inputs> + + <outputs> + <data format="bcf" name="output" label="BCF cat output"/> + </outputs> + + <help> +**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.) + + </help> + +</tool> \ No newline at end of file
--- /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 @@ +<tool id="BCF Tools Index" name="BCF Tools Index"> + <description>This tool allows the user to index sorted BCF for random access.</description> + + <requirements> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + + <command interpreter="python">bcftools index $input > $output </command> + + <inputs> + <param name="input" type="data" format="bcf" label="BCF File"/> + </inputs> + + <outputs> + <data format="bcf" name="output" label= "BCF index output"/> + </outputs> + + <help> +**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.) + + </help> + +</tool> \ No newline at end of file
--- /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 @@ +<tool id="bcftools_view" name="bcftools view" version="0.0.1"> + <description>Converts BCF format to VCF format</description> + <requirements> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <command interpreter="python"> + 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 + </command> + <inputs> + <param name="input" type="data" format="bcf" label="Choose a bcf file to view" /> + <param name="A" type="select" label="Retain all possible alternate alleles at variant sites"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="b" type="select" label="Output in the BCF format. The default is VCF."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <conditional name="D"> + <param name="seq_dictionary" type="select" label="Sequence dictionary (list of chromosome names) for VCF->BCF conversion."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="input" type="data" format="tabular" label="Sequence dictionary" /> + </when> + </conditional> + <param name="F" type="select" label="Indicate PL is generated by r921 or before (ordering is different)."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="G" type="select" label="Suppress all individual genotype information."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="N" type="select" label="Skip sites where the REF field is not A/C/G/T"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="S" type="select" label="The input is VCF instead of BCF."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="u" type="select" label="Uncompressed BCF output."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="c" type="select" label="Call variants using Bayesian inference. Automatically performs max-likelihood inference only"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <param name="e" type="select" label="Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="g" type="select" label="Call per-sample genotypes at variant sites"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <conditional name="i"> + <param name="alt_indel_snp_ratio" type="select" label="Use alternate INDEL-to-SNP mutation rate, default 0.15."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="ratio" type="float" label="Ratio (float)" value="0.15" /> + </when> + </conditional> + <conditional name="p"> + <param name="variant_filter" type="select" > + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="float_value" type="float" label="Float" value="0.5" /> + </when> + </conditional> + <conditional name="t"> + <param name="mutation_rate" type="select" label="Specify scaled mutation rate for variant calling, default is 0.001."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="rate" type="float" label="Mutation Rate (float)" value="0.001" /> + </when> + </conditional> + <param name="v" type="select" label="Output variant sites only."> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <help> +**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.) + + </help> +</tool>
--- /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 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.18"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bcftools/bcftools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Both BCFTools and Samtools installed in this dependency.Compiling SAMtools requires the ncurses and zlib development libraries.</readme> + </package> +</tool_dependency>