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freebayes4workflow.xml tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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diff -r 000000000000 -r 874dd6c0fcde freebayes4workflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/freebayes4workflow.xml Tue Nov 10 08:51:31 2015 -0500 |
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b'@@ -0,0 +1,851 @@\n+<?xml version="1.0"?>\n+<tool id="freebayes4workflow" name="Freebayes4Workflow" version="0.5">\n+ <requirements>\n+ <requirement type="package" version="1.0">freebayes</requirement>\n+ <requirement type="package" version="0.1.19">samtools</requirement>\n+ </requirements>\n+ <description> - bayesian genetic variant detector</description>\n+ <command>\n+ ##set up input files\n+\n+ #set $reference_fasta_filename = "localref.fa"\n+ \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+ \n+ #for $bam_count, $input_bam in enumerate( $input_bams ):\n+ ln -s "${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+ \n+ ## Tabixize optional input_varinat_vcf file (for --variant-input option)\n+ \n+ #if ( str( $options_type.options_type_selector ) == \'cline\' or str( $options_type.options_type_selector ) == \'full\' ) and $options_type.optional_inputs.optional_inputs_selector and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n+ ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&\n+ ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&\n+ #end if\n+ \n+ ##finished setting up inputs\n+ \n+ ##COMMAND LINE STARTS HERE\n+ \n+ freebayes\n+ #for $bam_count, $input_bam in enumerate( $input_bams ):\n+ --bam "localbam_${bam_count}.bam"\n+ #end for\n+ --fasta-reference "${reference_fasta_filename}"\n+ \n+ ##outputs\n+ #if str( $rename_output.rename_output_selector ) == "noRename":\n+ --vcf ${output_vcf_default}\n+ #elif str( $rename_output.rename_output_selector ) == "firstBAM":\n+ --vcf "${output_vcf_firstBAM}"\n+ #elif str( $rename_output.rename_output_selector ) == "providedName":\n+\t\t--vcf "${output_vcf_rename}"\n+ #end if\n+\n+ #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":\n+ --targets "${target_limit_type.input_target_bed}"\n+ #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":\n+ --region "${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}"\n+ #end if\n+ \n+ ##advanced options\n+ #if str( $options_type.options_type_selector ) == "simple":\n+ ##do nothing as command like build up to this point is sufficinet for simple diploid calling\n+ \n+ #elif str( $options_type.options_type_selector ) == "simple_w_filters":\n+ \n+ --standard-filters\n+ --min-coverage "${options_type.min_coverage}"\n+ \n+ #elif str( $options_type.options_type_selector ) == "naive":\n+ \n+ --haplotype-length 0\n+ --min-alternate-count 1\n+ --min-alternate-fraction 0\n+ --pooled-continuous\n+ --report-monomorphic\n+ \n+ #elif str( $options_type.options_type_selector ) == "naive_w_filters":\n+\n+ --haplotype-length 0\n+ --min-alternate-count 1\n+ --min-alternate-fraction 0\n+ --pooled-continuous\n+ --report-monomorphic\n+ --standard-filters\n+ --min-coverage "${options_type.min_coverage}"\n+\n+## Command line direct text entry is not allowed at this time for security reasons\n+ \n+ #elif str( $options_type.options_type_selector ) == "full":\n+ \n+ #if $options_type.optional_inputs.optional_inputs_selector:\n+ \n+ #if $options_type.optional_inputs.output_trace_option:\n+ --trace "${output_trace}"\n+ #end if\n+ '..b'ead placement probability, strand balance probability,\n+ and read position (5\'-3\') probability.\n+ -a --allele-balance-priors-off\n+ Disable use of aggregate probability of observation balance between alleles\n+ as a component of the priors.\n+\n+Genotype likelihoods::\n+\n+ --observation-bias FILE\n+ Read length-dependent allele observation biases from FILE.\n+ The format is [length] [alignment efficiency relative to reference]\n+ where the efficiency is 1 if there is no relative observation bias.\n+ --base-quality-cap Q\n+ Limit estimated observation quality by capping base quality at Q.\n+ --experimental-gls\n+ Generate genotype likelihoods using \'effective base depth\' metric\n+ qual = 1-BaseQual * 1-MapQual. Incorporate partial observations.\n+ This is the default when contamination estimates are provided.\n+ Optimized for diploid samples.\n+ --prob-contamination F\n+ An estimate of contamination to use for all samples. default: 10e-9\n+ --contamination-estimates FILE\n+ A file containing per-sample estimates of contamination, such as\n+ those generated by VerifyBamID. The format should be:\n+ sample p(read=R|genotype=AR) p(read=A|genotype=AA)\n+ Sample \'*\' can be used to set default contamination estimates.\n+\n+Algorithmic features::\n+\n+ --report-genotype-likelihood-max\n+ Report genotypes using the maximum-likelihood estimate provided\n+ from genotype likelihoods.\n+ -B --genotyping-max-iterations N\n+ Iterate no more than N times during genotyping step. default: 1000.\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+ -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+ -H --harmonic-indel-quality\n+ Use a weighted sum of base qualities around an indel, scaled by the\n+ distance from the indel. By default use a minimum BQ in flanking sequence.\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+ -= --genotype-qualities\n+ Calculate the marginal probability of genotypes and report as GQ in\n+ each sample field in the VCF output.\n+\n+\n+------\n+\n+**Citation**\n+\n+For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_.\n+\n+The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.\n+\n+ </help>\n+ \n+ <citations>\n+ <citation type="bibtex">@misc{1207.3907,\n+Author = {Erik Garrison},\n+Title = {Haplotype-based variant detection from short-read sequencing},\n+Year = {2012},\n+Eprint = {arXiv:1207.3907},\n+url = {http://arxiv.org/abs/1207.3907},\n+}</citation>\n+ </citations>\n+</tool>\n' |
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diff -r 000000000000 -r 874dd6c0fcde tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Tue Nov 10 08:51:31 2015 -0500 |
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@@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
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diff -r 000000000000 -r 874dd6c0fcde tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Nov 10 08:51:31 2015 -0500 |
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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 for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
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diff -r 000000000000 -r 874dd6c0fcde tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Nov 10 08:51:31 2015 -0500 |
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@@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="freebayes" version="1.0"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/freebayes/freebayes-0.9.20_b040236.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + </package> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |