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comparison freebayes.xml @ 20:ed8508ec9613 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
author iuc
date Wed, 07 May 2025 05:35:03 +0000
parents 3ccfc2851e21
children
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equal deleted inserted replaced
19:3ccfc2851e21 20:ed8508ec9613
1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
2 <description>bayesian genetic variant detector</description> 2 <description>bayesian genetic variant detector</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">freebayes</xref> 4 <xref type="bio.tools">freebayes</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
37 ln -s -f '${input_bam}' 'b_${bam_count}.cram' && 37 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
38 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' && 38 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
39 #end if 39 #end if
40 #end for 40 #end for
41 41
42 ## Tabixize optional input_variant_vcf file (for --variant-input option) 42 ## For --variant-input option, create symlinks to vcf.bgzip input and its accompanying tabix index
43 #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": 43 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
44 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz && 44 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
45 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi && 45 ln -s '$options_type.optional_inputs.input_variant_type.input_variant_vcf.metadata.tabix_index' input_variant_vcf.vcf.gz.tbi &&
46 #end if 46 #end if
47 47
48 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions 48 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
49 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file": 49 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
50 ln -s '${target_limit_type.input_target_bed}' regions_all.bed && 50 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
127 #end if 127 #end if
128 #if $options_type.optional_inputs.A: 128 #if $options_type.optional_inputs.A:
129 --cnv-map '${options_type.optional_inputs.A}' 129 --cnv-map '${options_type.optional_inputs.A}'
130 #end if 130 #end if
131 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf": 131 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
132 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above 132 --variant-input 'input_variant_vcf.vcf.gz'
133 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles} 133 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
134 #end if 134 #end if
135 #if $options_type.optional_inputs.haplotype_basis_alleles: 135 #if $options_type.optional_inputs.haplotype_basis_alleles:
136 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}' 136 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
137 #end if 137 #end if
363 <option value="provide_vcf">Provide VCF dataset</option> 363 <option value="provide_vcf">Provide VCF dataset</option>
364 </param> 364 </param>
365 <when value="do_not_provide" /> 365 <when value="do_not_provide" />
366 <when value="provide_vcf"> 366 <when value="provide_vcf">
367 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip" 367 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
368 label="Use variants reported in this VCF dataset as input to the algorithm"> 368 label="Use variants reported in this VCF dataset as input to the algorithm"/>
369 <conversion name="Tabixized_input" type="tabix" />
370 </param>
371 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false" 369 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
372 label="Only provide variant calls and genotype likelihoods for sites in VCF" /> 370 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
373 </when> 371 </when>
374 </conditional> 372 </conditional>
375 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true" 373 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
638 <param name="options_type_selector" value="naive_w_filters"/> 636 <param name="options_type_selector" value="naive_w_filters"/>
639 <param name="coverage_options_selector" value="set" /> 637 <param name="coverage_options_selector" value="set" />
640 <param name="min_coverage" value="14"/> 638 <param name="min_coverage" value="14"/>
641 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" /> 639 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
642 </test> 640 </test>
641 <!-- Test that user-provided (variant-input option) sites are included in output -->
643 <test> 642 <test>
644 <param name="reference_source_selector" value="history" /> 643 <param name="reference_source_selector" value="history" />
645 <param name="processmode" value="individual" /> 644 <param name="processmode" value="individual" />
646 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> 645 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
647 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/> 646 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
648 <param name="options_type_selector" value="naive_w_filters"/> 647 <param name="options_type_selector" value="full"/>
649 <param name="coverage_options_selector" value="set" /> 648 <conditional name="optional_inputs">
650 <param name="min_coverage" value="14"/> 649 <param name="optional_inputs_selector" value="set" />
651 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" /> 650 <conditional name="input_variant_type">
651 <param name="input_variant_type_selector" value="provide_vcf" />
652 <param name="input_variant_vcf" value="freebayes-phix174-input-sites-test3.vcf.bgzip" />
653 </conditional>
654 </conditional>
655 <output name="output_vcf">
656 <assert_contents>
657 <has_line_matching expression="phiX174&#009;1134&#009;\.&#009;A&#009;\.&#009;.+"/>
658 </assert_contents>
659 </output>
652 </test> 660 </test>
653 <test> 661 <test>
654 <param name="reference_source_selector" value="history" /> 662 <param name="reference_source_selector" value="history" />
655 <param name="processmode" value="individual" /> 663 <param name="processmode" value="individual" />
656 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> 664 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>