| Next changeset 1:046c7983e2ff (2012-07-02) |
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Commit message:
Uploaded freebayes with tool dependencies |
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added:
freebayes.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 61fe907fc37c freebayes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/freebayes.xml Mon Jul 02 17:49:47 2012 -0400 |
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| b'@@ -0,0 +1,670 @@\n+<?xml version="1.0"?>\n+<tool id="freebayes" name="FreeBayes" version="0.0.2">\n+ <requirements>\n+ <requirement type="package" version="0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8">freebayes</requirement>\n+ <requirement type="package" version="0.1.18">samtools</requirement>\n+ </requirements>\n+ <description> - Bayesian genetic variant detector</description>\n+ <command>\n+ ##set up input files\n+ #set $reference_fasta_filename = "localref.fa"\n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n+ samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&\n+ #else:\n+ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n+ #end if\n+ #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):\n+ ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&\n+ ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&\n+ #end for\n+ ##finished setting up inputs\n+ \n+ ##start FreeBayes commandline\n+ freebayes\n+ #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):\n+ --bam "localbam_${bam_count}.bam"\n+ #end for\n+ --fasta-reference "${reference_fasta_filename}" \n+ \n+ ##outputs\n+ --vcf "${output_vcf}"\n+ \n+ ##advanced options\n+ #if str( $options_type.options_type_selector ) == "advanced":\n+ ##additional outputs\n+ #if $options_type.output_trace_option:\n+ --trace "${output_trace}"\n+ #end if\n+ #if $options_type.output_failed_alleles_option:\n+ --failed-alleles "${output_failed_alleles_bed}"\n+ #end if\n+ \n+ ##additional inputs\n+ #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file":\n+ --targets "${options_type.target_limit_type.input_target_bed}"\n+ #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region":\n+ --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}"\n+ #end if\n+ #if $options_type.input_sample_file:\n+ --samples "${options_type.input_sample_file}"\n+ #end if\n+ #if $options_type.input_populations_file:\n+ --populations "${options_type.input_populations_file}"\n+ #end if\n+ #if $options_type.input_cnv_map_bed:\n+ --cnv-map "${options_type.input_cnv_map_bed}"\n+ #end if\n+ #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n+ --variant-input "${options_type.input_variant_type.input_variant_vcf}"\n+ ${options_type.input_variant_type.only_use_input_alleles}\n+ #end if\n+ \n+ ##reporting\n+ #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":\n+ --pvar "${options_type.section_reporting_type.pvar}"\n+ ${options_type.section_reporting_type.show_reference_repeats}\n+ #end if\n+ \n+ ##population model\n+ #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set":\n+ --theta "${options_type.section_population_model_type.theta}"\n+ --ploidy "${options_type.section_population_model_type.ploidy}"\n+ ${options_type.section_population_model_type.pooled}\n+ #end if\n+ \n+ ##reference allele\n+ #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele":\n+ --use-reference-allele\n+ ${options_type.use_reference_allele_type.diploid_reference}\n+ --reference-qual'..b" an alternate allele within a single individual in order\n+ to evaluate the position. default: 1\n+ -3 --min-alternate-qsum N\n+ Require at least this sum of quality of observations supporting\n+ an alternate allele within a single individual in order\n+ to evaluate the position. default: 0\n+ -G --min-alternate-total N\n+ Require at least this count of observations supporting\n+ an alternate allele within the total population in order\n+ to use the allele in analysis. default: 1\n+ -! --min-coverage N\n+ Require at least this coverage to process a site. default: 0\n+\n+ bayesian priors:\n+\n+ -Y --no-ewens-priors\n+ Turns off the Ewens' Sampling Formula component of the priors.\n+ -k --no-population-priors\n+ Equivalent to --pooled --no-ewens-priors\n+ -w --hwe-priors Use the probability of the combination arising under HWE given\n+ the allele frequency as estimated by observation frequency.\n+\n+ observation prior expectations:\n+\n+ -V --binomial-obs-priors\n+ Incorporate expectations about osbervations into the priors,\n+ Uses read placement probability, strand balance probability,\n+ and read position (5'-3') probability.\n+ -a --allele-balance-priors\n+ Use aggregate probability of observation balance between alleles\n+ as a component of the priors. Best for observations with minimal\n+ inherent reference bias.\n+\n+ algorithmic features:\n+\n+ -M --site-selection-max-iterations N\n+ Uses hill-climbing algorithm to search posterior space for N\n+ iterations to determine if the site should be evaluated. Set to 0\n+ to prevent use of this algorithm for site selection, and\n+ to a low integer for improvide site selection at a slight\n+ performance penalty. default: 5.\n+ -B --genotyping-max-iterations N\n+ Iterate no more than N times during genotyping step. default: 25.\n+ --genotyping-max-banddepth N\n+ Integrate no deeper than the Nth best genotype by likelihood when\n+ genotyping. default: 6.\n+ -W --posterior-integration-limits N,M\n+ Integrate all genotype combinations in our posterior space\n+ which include no more than N samples with their Mth best\n+ data likelihood. default: 1,3.\n+ -K --no-permute\n+ Do not scale prior probability of genotype combination given allele\n+ frequency by the number of permutations of included genotypes.\n+ -N --exclude-unobserved-genotypes\n+ Skip sample genotypings for which the sample has no supporting reads.\n+ -S --genotype-variant-threshold N\n+ Limit posterior integration to samples where the second-best\n+ genotype likelihood is no more than log(N) from the highest\n+ genotype likelihood for the sample. default: ~unbounded\n+ -j --use-mapping-quality\n+ Use mapping quality of alleles when calculating data likelihoods.\n+ -D --read-dependence-factor N\n+ Incorporate non-independence of reads by scaling successive\n+ observations by this factor during data likelihood\n+ calculations. default: 0.9\n+ -= --no-marginals\n+ Do not calculate the marginal probability of genotypes. Saves\n+ time and improves scaling performance in large populations.\n+\n+\n+------\n+\n+**Citation**\n+\n+For the underlying tool, please cite `FreeBayes <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_.\n+\n+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n+\n+ </help>\n+</tool>\n" |
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| diff -r 000000000000 -r 61fe907fc37c tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jul 02 17:49:47 2012 -0400 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes and other files --> + <table name="sam_fa_indexes" comment_char="#"> + <columns>line_type, value, path</columns> + <file path="tool-data/sam_fa_indices.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 61fe907fc37c tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jul 02 17:49:47 2012 -0400 |
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| @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="freebayes" version="0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> + <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +FreeBayes requires g++ and the standard C and C++ development libraries. +Additionally, cmake is required for building the BamTools API. + </readme> + </package> + <package name="samtools" version="0.1.18"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> + <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>misc/maq2sam-long</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> +Compiling SAMtools requires the ncurses and zlib development libraries. + </readme> + </package> +</tool_dependency> |