| Previous changeset 7:b03984136ce4 (2017-12-12) Next changeset 9:cb30a39055d0 (2019-06-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 |
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modified:
bcftools_call.xml macros.xml test-data/view.bcf |
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added:
test-data/summary.pdf test-data/view.vcf_bgzip |
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removed:
test-data/view.bcf.csi |
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| diff -r b03984136ce4 -r 0fba2c15b40d bcftools_call.xml --- a/bcftools_call.xml Tue Dec 12 14:05:16 2017 -0500 +++ b/bcftools_call.xml Thu Feb 21 16:09:28 2019 -0500 |
| [ |
| b'@@ -1,16 +1,16 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">\n+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">\n <description>SNP/indel variant calling from VCF/BCF</description>\n <macros>\n <token name="@EXECUTABLE@">call</token>\n <import>macros.xml</import>\n <xml name="macro_novel_rate">\n- <param name="novel_rate_snp" type="float" label="Novel Rate SNP" value="" optional="true" \n- help="likelihood of novel mutation for constrained trio calling, see man page for details" />\n- <param name="novel_rate_del" type="float" label="Novel Rate Deletions" value="" optional="true" \n- help="likelihood of novel mutation for constrained trio calling, see man page for details" />\n- <param name="novel_rate_ins" type="float" label="Novel Rate Insertions" value="" optional="true" \n- help="likelihood of novel mutation for constrained trio calling, see man page for details" />\n+ <param name="novel_rate_snp" type="float" value="" optional="true" label="Novel rate for SNPs"\n+ help="Likelihood of novel mutation for constrained trio calling, see man page for details" />\n+ <param name="novel_rate_del" type="float" value="" optional="true" label="Novel rate for deletions"\n+ help="Likelihood of novel mutation for constrained trio calling, see man page for details" />\n+ <param name="novel_rate_ins" type="float" value="" optional="true" label="Novel rate for insertions"\n+ help="Likelihood of novel mutation for constrained trio calling, see man page for details" />\n </xml>\n <token name="@NOVEL_RATE@">\n #set $novel_rate = []\n@@ -36,10 +36,10 @@\n #set $section = $sec_consensus_variant_calling.variant_calling\n #set $targets_path = None\n #if $section.method == \'multiallelic\':\n- #if $section.genotypes.constrain == \'alleles\': \n- #set $section = $sec_consensus_variant_calling.variant_calling.genotypes\n- @PREPARE_TARGETS_FILE@\n- #end if\n+ #if $section.genotypes.constrain == \'alleles\':\n+ #set $section = $sec_consensus_variant_calling.variant_calling.genotypes\n+ @PREPARE_TARGETS_FILE@\n+ #end if\n #end if\n #set $section = $sec_restrict\n @PREPARE_REGIONS_FILE@\n@@ -48,59 +48,57 @@\n \n #set $section = $sec_consensus_variant_calling.variant_calling\n #if $section.method == \'multiallelic\':\n- -m\n- #if str($section.gvcf) != \'\':\n- --gvcf $section.gvcf\n- #end if\n- #if str($section.prior_freqs) != \'\':\n- --prior-freqs $section.prior_freqs\n- #end if\n- #if $section.genotypes.constrain == \'alleles\': \n- --constrain alleles $section.genotypes.insert_missed\n- #set $section = $sec_consensus_variant_calling.variant_calling.genotypes\n- @TARGETS_FILE@\n- #else\n- #if $section.genotypes.constrain == \'trio\':\n- --constrain trio\n- @NOVEL_RATE@\n- #end if\n- #set $section = $sec_consensus_variant_calling.variant_calling.genotypes\n- @TARGETS@\n- #end if\n-#else \n- -c\n+ -m\n+ #if str($section.gvcf):\n+ --gvcf $section.gvcf\n+ #end if\n+ #if str($section.prior_freqs):\n+ --prior-freqs \'$section.prior_freqs\'\n+ #end if\n+ #if str($section.prior):\n+ --prior $section.prior\n+ #end if\n+ #if $section.genotypes.constrain == \'alleles\':\n+ --constrain alleles $section.genotypes.insert_missed\n+ #set $section = $sec_consensus_variant_calling.variant_calling.genotypes\n+ @TARGETS_FILE@\n+ #else\n+ #if $section.genotypes.constrain == \'trio\':\n+ --constrain trio\n+ @NOVEL_RATE@\n+ #end if\n+ #set $section = $sec_consensus_variant_calling.variant_calling.genotypes\n+ @TARGETS@\n+ #end if\n+#else\n+ -c\n+ #if str($section.pval_threshold):\n+ --pval-threshold $section.pval_threshold\n+ #end if\n #end if\n \n #set $sectio'..b'ey do not appear in any of the genotypes" />\n+ <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"\n+ help="Currently GQ and GP fields are supported" >\n <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>\n </param>\n- <param name="keep_masked_ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep Masked Ref" help="keep sites with masked reference allele (REF=N)" />\n- <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps">\n+ <param name="keep_masked_ref" argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" />\n+ <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">\n <option value="indels">indels</option>\n <option value="snps">snps</option>\n </param>\n- <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" />\n+ <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />\n </section>\n <expand macro="macro_select_output_type" />\n </inputs>\n@@ -258,13 +254,13 @@\n bcftools @EXECUTABLE@\n ==================================\n \n-SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup. \n+SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.\n \n- - This command replaces the former "bcftools view" caller. \n- - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. \n+ - This command replaces the former "bcftools view" caller.\n+ - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand.\n - The original calling model can be invoked with the -c option.\n \n-The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels. \n+The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels.\n \n \n @REGIONS_HELP@\n' |
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| diff -r b03984136ce4 -r 0fba2c15b40d macros.xml --- a/macros.xml Tue Dec 12 14:05:16 2017 -0500 +++ b/macros.xml Thu Feb 21 16:09:28 2019 -0500 |
| [ |
| b'@@ -1,5 +1,5 @@\n <macros>\n- <token name="@VERSION@">1.4.0</token>\n+ <token name="@TOOL_VERSION@">1.9</token>\n <xml name="stdio">\n <stdio>\n <exit_code range="1:" />\n@@ -10,13 +10,13 @@\n </xml>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.4">bcftools</requirement>\n- <requirement type="package" version="1.4">htslib</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>\n+ <requirement type="package" version="1.9">htslib</requirement>\n <yield />\n </requirements>\n </xml>\n <xml name="samtools_requirement">\n- <requirement type="package" version="1.3.1">samtools</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n </xml>\n <xml name="version_command">\n <version_command>bcftools 2>&1 | grep \'Version:\'</version_command>\n@@ -39,7 +39,7 @@\n ]]>\n </token>\n <xml name="macro_input">\n- <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />\n+ <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />\n </xml>\n <token name="@PREPARE_INPUT_FILE@">\n <![CDATA[\n@@ -50,6 +50,11 @@\n bcftools index $input_vcf &&\n #elif $input_file.is_of_type(\'vcf_bgzip\')\n ln -s \'$input_file\' $input_vcf &&\n+ #if $input_file.metadata.tabix_index:\n+ ln -s \'${input_file.metadata.tabix_index}\' ${input_vcf}.tbi &&\n+ #else\n+ bcftools index $input_vcf &&\n+ #end if\n #elif $input_file.is_of_type(\'bcf\')\n #set $input_vcf = \'input.bcf\'\n ln -s \'$input_file\' $input_vcf &&\n@@ -58,8 +63,6 @@\n #else\n bcftools index $input_vcf &&\n #end if\n-#elif $input_file.is_of_type(\'bcf_bgzip\')\n- ln -s \'$input_file\' $input_vcf &&\n #end if\n ]]>\n </token>\n@@ -68,7 +71,7 @@\n </token>\n \n <xml name="macro_inputs">\n- <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />\n+ <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />\n </xml>\n <token name="@PREPARE_INPUT_FILES@">\n <![CDATA[\n@@ -80,8 +83,13 @@\n #if $input_file.is_of_type(\'vcf\')\n bgzip -c \'$input_file\' > $input_vcf &&\n bcftools index $input_vcf &&\n- #elif $input_file.is_of_type(\'vcf_bgz\')\n- ln -s \'$input_file\' $input_vcf\n+ #elif $input_file.is_of_type(\'vcf_bgzip\')\n+ ln -s \'$input_file\' $input_vcf &&\n+ #if $input_file.metadata.tabix_index:\n+ ln -s \'${input_file.metadata.tabix_index}\' ${input_vcf}.tbi &&\n+ #else\n+ bcftools index $input_vcf &&\n+ #end if\n #elif $input_file.is_of_type(\'bcf\')\n #set $input_vcf = \'input\' + str($i) + \'.bcf.gz\'\n ln -s \'$input_file\' $input_vcf &&\n@@ -90,8 +98,6 @@\n #else\n bcftools index $input_vcf &&\n #end if\n- #elif $input_file.is_of_type(\'bcfvcf_bgz\')\n- ln -s \'$input_file\' $input_vcf &&\n #end if\n echo \'$input_vcf\' >> $vcfs_list_file &&\n $input_vcfs.append($input_vcf)\n@@ -106,7 +112,7 @@\n </token>\n \n <xml name="macro_fasta_ref">\n- <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />\n+ <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />\n </xml>\n <token name="@PREPARE_FASTA_REF@">\n <![CDATA[\n@@ -148,7 +154,7 @@\n \n \n <xml name="macro_AF_file">\n- <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />\n+ <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />\n </xml>\n <!-- This may need to bgzip and tabix the file -->\n <token name="@PREPARE_AF_FILE@">\n@@ -165,7 +171,7 @@\n </token>\n \n <xml '..b'ne__"/>\n <when value="targets">\n- <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"\n+ <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"\n help="Each target is specifed as: chr or chr:pos or chr:from-to">\n <validator type="regex" message="">^(\\w+(:\\d+(-\\d+)?)?(,\\w+(:\\d+(-\\d+)?)?)*)?$</validator>\n </param>\n@@ -373,16 +379,16 @@\n </token>\n \n <xml name="macro_samples">\n- <param name="samples" type="text" value="" label="Samples" optional="true"\n- help="(-s) comma separated list of samples to annotate (or exclude)">\n+ <param argument="--samples" type="text" value="" optional="true" label="Samples"\n+ help="Comma separated list of samples to annotate (or exclude)">\n <validator type="regex" message="">^(\\w+(,\\w+)*)?$</validator>\n </param>\n <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"\n- help="inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />\n- <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"\n- help="(-S) file of samples to include" />\n- <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"\n- help="inverts the query/filtering applied by Samples File" />\n+ help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />\n+ <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"\n+ help="File of samples to include" />\n+ <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"\n+ help="inverts the query/filtering applied by Samples file" />\n </xml>\n <token name="@SAMPLES@">\n #set $samples_defined = False\n@@ -397,7 +403,7 @@\n </token>\n \n <xml name="macro_sample">\n- <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />\n+ <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />\n </xml>\n <token name="@SAMPLE@">\n #if $section.sample:\n@@ -407,7 +413,7 @@\n \n \n <xml name="macro_include">\n- <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">\n+ <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">\n <validator type="regex" message="Single quote not allowed">^[^\']*$</validator>\n <sanitizer sanitize="False"/>\n </param>\n@@ -419,7 +425,7 @@\n </token>\n \n <xml name="macro_exclude">\n- <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">\n+ <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">\n <validator type="regex" message="Single quote not allowed">^[^\']*$</validator>\n <sanitizer sanitize="False"/>\n </param>\n@@ -431,8 +437,8 @@\n </token>\n \n <xml name="macro_columns">\n- <param name="columns" type="text" value="" label="Columns" optional="true"\n- help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">\n+ <param name="columns" type="text" value="" optional="true" label="Columns"\n+ help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">\n <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>\n </param>\n </xml>\n' |
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