| Previous changeset 27:9f164587a92f (2017-06-06) Next changeset 29:156b60c1530f (2017-10-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214 |
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modified:
freebayes.xml leftalign.xml macros.xml test-data/left-align-output.bam |
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| diff -r 9f164587a92f -r 977a5301b66d freebayes.xml --- a/freebayes.xml Tue Jun 06 11:44:38 2017 -0400 +++ b/freebayes.xml Tue Jun 06 18:41:18 2017 -0400 |
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| b'@@ -1,18 +1,13 @@\n-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">\n+<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-1">\n <description>bayesian genetic variant detector</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>\n- <requirement type="package" version="0.1.19">samtools</requirement>\n+ <expand macro="requirements">\n <requirement type="package" version="4.1.3">gawk</requirement>\n <requirement type="package" version="20160622">parallel</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command><![CDATA[\n+ </expand>\n+ <command detect_errors="exit_code"><![CDATA[\n ##set up input files\n \n #set $reference_fasta_filename = "localref.fa"\n@@ -37,12 +32,11 @@\n \n ## Tabixize optional input_variant_vcf file (for --variant-input option)\n #if ( str( $options_type.options_type_selector ) == \'cline\' or str( $options_type.options_type_selector ) == \'full\' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == \'set\' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":\n- ln -s -f \'${options_type.optional_inputs.input_variant_type.input_variant_vcf}\' \'input_variant_vcf.vcf.gz\' &&\n- ln -s -f \'${Tabixized_input}\' \'input_variant_vcf.vcf.gz.tbi\' &&\n+ ln -s -f \'${options_type.optional_inputs.input_variant_type.input_variant_vcf}\' input_variant_vcf.vcf.gz &&\n+ ln -s -f \'${Tabixized_input}\' input_variant_vcf.vcf.gz.tbi &&\n #end if\n \n- ##if user has specified a region or target file, just use instead of calculating a set of unique regions\n-\n+ ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions\n #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":\n ln -s \'${target_limit_type.input_target_bed}\' regions_all.bed &&\n #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":\n@@ -51,11 +45,9 @@\n ##divide up the regions in the bam file for efficient processing\n #for $bam_count, $input_bam in enumerate( $input_bamfiles ):\n samtools view -H b_${bam_count}.bam |\n- grep "^@SQ" |\n+ grep \'^@SQ\' |\n cut -f 2- |\n- awk \'{ gsub("^SN:","",$1);\n- gsub("^LN:","",$2);\n- print $1"\\t0\\t"$2; }\' >> regions_all.bed &&\n+ awk \'{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\\t0\\t"$2; }\' >> regions_all.bed &&\n #end for\n #end if\n \n@@ -63,15 +55,12 @@\n ## split into even small chunks, this has some disatvantages and will not be used for the moment\n ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&\n \n- mkdir vcf_output &&\n- mkdir failed_alleles &&\n- mkdir trace &&\n+ mkdir vcf_output failed_alleles trace &&\n \n ## Finished setting up inputs\n \n for i in `cat regions_uniq.bed | awk \'{print $1":"$2".."$3}\'`;\n do\n-\n echo "\n \n ## COMMAND LINE STARTS HERE\n@@ -90,11 +79,10 @@\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+ #pass\n #elif str( $options_type.options_type_selector ) == "simple_w_filters":\n --standard-filters\n- --min-coverage \'${options_type.min_coverage}\'\n+ --min-coverage ${options_type.min_coverage}\n #elif str( $options_type.options_type_selector ) == "naive":\n --haplotype-length 0\n --min-alternate-count 1\n@@ -108,9 +96,7 @@\n --pooled-continuous\n --report-monomorphic\n --standard-filters'..b' 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+ 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.\n+ 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-variant-threshold 0) and --min-coverage.\n+ 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling variants in mixtures such as viral, bacterial, or organellar genomes.\n+ 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.\n+ 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.\n \n ------\n \n **Acknowledgments**\n \n The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.\n-TNG was developed by Bjoern Gruening\n+TNG was developed by Bjoern Gruening.\n </help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 9f164587a92f -r 977a5301b66d leftalign.xml --- a/leftalign.xml Tue Jun 06 11:44:38 2017 -0400 +++ b/leftalign.xml Tue Jun 06 18:41:18 2017 -0400 |
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| @@ -1,17 +1,11 @@ <?xml version="1.0"?> -<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@-1"> +<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@-2"> <description> indels in BAM datasets</description> <macros> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="1.0.2.29">freebayes</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command><![CDATA[ + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ ##set up input files #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": |
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| diff -r 9f164587a92f -r 977a5301b66d macros.xml --- a/macros.xml Tue Jun 06 11:44:38 2017 -0400 +++ b/macros.xml Tue Jun 06 18:41:18 2017 -0400 |
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| @@ -1,6 +1,12 @@ <macros> <token name="@DEPENDENCY_VERSION@">1.1.0</token> - + <xml name="requirements"> + <requirements> + <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + <yield /> + </requirements> + </xml> <xml name="citations"> <citations> <citation type="bibtex"> @@ -20,24 +26,23 @@ </xml> <xml name="input_bam"> <conditional name="batchmode"> - <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF file for each input BAM file. Selecting the merge option will produce one VCF file for all input BAM files." display="radio"> - <option value="individual" selected="True">Run individually</option> + <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF dataset for each input BAM dataset. Selecting the merge option will produce one VCF dataset for all input BAM datasets" display="radio"> + <option value="individual" selected="true">Run individually</option> <option value="merge">Merge output VCFs</option> </param> <when value="individual"> - <param name="input_bams" type="data" format="bam" label="BAM file"> + <param name="input_bams" type="data" format="bam" label="BAM dataset"> <yield /> </param> </when> <when value="merge"> - <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file"> + <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)"> <yield /> </param> </when> </conditional> </xml> <xml name="par_min_cov"> - <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" - help="default=0" argument="--coverage" /> + <param name="min_coverage" argument="--coverage" type="integer" value="0" label="Require at least this coverage to process a site" /> </xml> </macros> |
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| diff -r 9f164587a92f -r 977a5301b66d test-data/left-align-output.bam |
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| Binary file test-data/left-align-output.bam has changed |