| Previous changeset 1:9c711df3258d (2017-12-12) Next changeset 3:4e1d23e5c691 (2019-05-27) |
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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_mpileup.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 9c711df3258d -r cf06b44624c7 bcftools_mpileup.xml --- a/bcftools_mpileup.xml Tue Dec 12 14:05:31 2017 -0500 +++ b/bcftools_mpileup.xml Thu Feb 21 16:09:57 2019 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> <macros> <token name="@EXECUTABLE@">mpileup</token> @@ -16,7 +16,7 @@ <option value="256">The alignment or this read is not primary</option> <option value="512">The read fails platform/vendor quality checks</option> <option value="1024">The read is a PCR or optical duplicate</option> - </xml> + </xml> </macros> <expand macro="requirements"> <expand macro="samtools_requirement"/> @@ -37,9 +37,9 @@ #silent $bam_list.append($input_name) ln -s '${input.input_bam}' ${input_name} && #if $input.input_bam.ext == 'bam': - ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} && + ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} && #else: - ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} && + ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} && #end if #else: #for $bam_count, $input_bam in enumerate( $input.input_bams ): @@ -59,11 +59,11 @@ #set $input_fa_ref = None #if $reference_source.reference_source_selector == "history": - #set $input_fa_ref = 'ref.fa' - ln -s '${reference_source.ref_file}' $input_fa_ref && - samtools faidx $input_fa_ref && + #set $input_fa_ref = 'ref.fa' + ln -s '${reference_source.ref_file}' $input_fa_ref && + samtools faidx $input_fa_ref && #elif $reference_source.reference_source_selector == "cached": - #set $input_fa_ref = $reference_source.ref_file.fields.path + #set $input_fa_ref = $reference_source.ref_file.fields.path #end if #set $section = $sec_restrict @@ -81,53 +81,53 @@ ## Indel Calling section #set $section = $sec_indel #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling': - --skip-indels + --skip-indels #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling': - -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}" - -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}" - -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" - -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}" - -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" - --open-prob "${section.perform_indel_calling.open_seq_error_probability}" - -F "${section.perform_indel_calling.minimum_gapped_read_fraction}" - ${section.perform_indel_calling.gapped_read_per_sample} - #if len( $section.perform_indel_calling.platform_list_repeat ): - -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }" - #end if + -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}" + -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}" + -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" + -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}" + -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" + --open-prob "${section.perform_indel_calling.open_seq_error_probability}" + -F "${section.perform_indel_calling.minimum_gapped_read_fraction}" + ${section.perform_indel_calling.gapped_read_per_sample} + #if len( $section.perform_indel_calling.platform_list_repeat ): + -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }" + #end if #end if ## Filter section #set $section = $sec_filtering #if str( $section.filter_by_flags.filter_flags ) == "filter": - #if $section.filter_by_flags.require_flags: - --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])} - #end if - #if $section.filter_by_flags.exclude_flags: - --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])} - #end if + #if $section.filter_by_flags.require_flags: + --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])} + #end if + #if $section.filter_by_flags.exclude_flags: + --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])} + #end if #end if -d "${section.max_reads_per_bam}" ${section.skip_anomalous_read_pairs} #if str( $section.quality.quality_settings ) == "adjust": - $section.quality.baq - -q "${section.quality.minimum_mapping_quality}" - -Q "${section.quality.minimum_base_quality}" - -C "${section.quality.coefficient_for_downgrading}" + $section.quality.baq + -q "${section.quality.minimum_mapping_quality}" + -Q "${section.quality.minimum_base_quality}" + -C "${section.quality.coefficient_for_downgrading}" #end if #if str( $section.read_groups.read_groups_selector ) == "ignore_rg": - --ignore-RG + --ignore-RG #elif str( $section.read_groups.read_groups_selector ) == "paste": - -G "${section.read_groups.rg_action}${read_groups_file}" + -G "${section.read_groups.rg_action}${read_groups_file}" #elif str( $section.read_groups.read_groups_selector ) == "history" - -G "${section.read_groups.rg_action}${section.read_groups.read_groups}" + -G "${section.read_groups.rg_action}${section.read_groups.read_groups}" #end if #set $section = $sec_output_options #if $section.output_tags: - --annotate "$section.output_tags" + --annotate "$section.output_tags" #end if #if $section.gvcf: - --gvcf "$section.gvcf" + --gvcf "$section.gvcf" #end if ## Subset section @@ -147,18 +147,17 @@ #echo ' '.join($bam_list)# > '$output_file' #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste": -&& echo 'read-groups:' -&& cat ${read_groups_file} + && echo 'read-groups:' + && cat ${read_groups_file} #end if -]]> - </command> + ]]></command> <configfiles> <configfile name="read_groups_file"> <![CDATA[#slurp #set pasted_data = '' #set $section = $sec_filtering #if str( $section.read_groups.read_groups_selector ) == "paste": - #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() ) + #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() ) #end if #slurp ${pasted_data} @@ -444,7 +443,6 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ @BCFTOOLS_WIKI@ -]]> - </help> + ]]></help> <expand macro="citations" /> </tool> |
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| diff -r 9c711df3258d -r cf06b44624c7 macros.xml --- a/macros.xml Tue Dec 12 14:05:31 2017 -0500 +++ b/macros.xml Thu Feb 21 16:09:57 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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| diff -r 9c711df3258d -r cf06b44624c7 test-data/summary.pdf |
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| diff -r 9c711df3258d -r cf06b44624c7 test-data/view.bcf |
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| diff -r 9c711df3258d -r cf06b44624c7 test-data/view.bcf.csi |
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| diff -r 9c711df3258d -r cf06b44624c7 test-data/view.vcf_bgzip |
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