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comparison freebayes.xml @ 14:91271de440f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
author iuc
date Wed, 01 Dec 2021 21:49:34 +0000
parents 5031b6656a2b
children c3da1614f96d
comparison
equal deleted inserted replaced
13:5031b6656a2b 14:91271de440f0
1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
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>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements"> 9 <expand macro="requirements">
10 <requirement type="package" version="4.1.3">gawk</requirement> 10 <requirement type="package" version="5.1.0">gawk</requirement>
11 <requirement type="package" version="20170422">parallel</requirement> 11 <requirement type="package" version="20211022">parallel</requirement>
12 </expand> 12 </expand>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 ##set up input files 14 ##set up input files
15 15
16 #set $reference_fasta_filename = "localref.fa" 16 #set $reference_fasta_filename = "localref.fa"
27 #else: 27 #else:
28 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ] 28 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
29 #end if 29 #end if
30 30
31 #for $bam_count, $input_bam in enumerate( $input_bamfiles ): 31 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
32 ln -s -f '${input_bam}' 'b_${bam_count}.bam' && 32 #if $input_bam.ext == 'bam':
33 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' && 33 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
34 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
35 #elif $input_bam.ext == 'cram':
36 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
37 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
38 #end if
34 #end for 39 #end for
35 40
36 ## Tabixize optional input_variant_vcf file (for --variant-input option) 41 ## Tabixize optional input_variant_vcf file (for --variant-input option)
37 #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": 42 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
38 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz && 43 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
45 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region": 50 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
46 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed && 51 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
47 #else 52 #else
48 ##divide up the regions in the bam file for efficient processing 53 ##divide up the regions in the bam file for efficient processing
49 #for $bam_count, $input_bam in enumerate( $input_bamfiles ): 54 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
50 samtools view -H b_${bam_count}.bam | 55 samtools view -H b_${bam_count}.${input_bam.ext}|
51 grep '^@SQ' | 56 grep '^@SQ' |
52 cut -f 2- | 57 cut -f 2- |
53 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed && 58 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
54 #end for 59 #end for
55 #end if 60 #end if
71 freebayes 76 freebayes
72 77
73 --region '\$i' 78 --region '\$i'
74 79
75 #for $bam_count, $input_bam in enumerate( $input_bamfiles ): 80 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
76 --bam 'b_${bam_count}.bam' 81 --bam 'b_${bam_count}.${input_bam.ext}'
77 #end for 82 #end for
78 --fasta-reference '${reference_fasta_filename}' 83 --fasta-reference '${reference_fasta_filename}'
79 84
80 ## Outputs 85 ## Outputs
81 --vcf './vcf_output/part_\$i.vcf' 86 --vcf './vcf_output/part_\$i.vcf'
133 --observation-bias '${options_type.optional_inputs.observation_bias}' 138 --observation-bias '${options_type.optional_inputs.observation_bias}'
134 #end if 139 #end if
135 #if $options_type.optional_inputs.contamination_estimates: 140 #if $options_type.optional_inputs.contamination_estimates:
136 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}' 141 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
137 #end if 142 #end if
143 $options_type.optional_inputs.trim_complex_tail
138 #end if 144 #end if
139 145
140 ## REPORTING 146 ## REPORTING
141 #if str( $options_type.reporting.reporting_selector ) == "set": 147 #if str( $options_type.reporting.reporting_selector ) == "set":
142 --pvar ${options_type.reporting.pvar} 148 --pvar ${options_type.reporting.pvar}
330 </param> 336 </param>
331 <when value="full"> 337 <when value="full">
332 338
333 <conditional name="optional_inputs"> 339 <conditional name="optional_inputs">
334 <param name="optional_inputs_selector" type="select" label="Additional inputs" 340 <param name="optional_inputs_selector" type="select" label="Additional inputs"
335 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates"> 341 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail">
336 <option value="do_not_set" selected="true">Do not provide additional inputs</option> 342 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
337 <option value="set">Provide additional inputs</option> 343 <option value="set">Provide additional inputs</option>
338 </param> 344 </param>
339 <when value="set"> 345 <when value="set">
340 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false" 346 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
373 label="Load read length-dependent allele observation biases from" 379 label="Load read length-dependent allele observation biases from"
374 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" /> 380 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
375 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true" 381 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
376 label="Upload per-sample estimates of contamination from" 382 label="Upload per-sample estimates of contamination from"
377 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" /> 383 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" />
384 <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
385 label="Trim trailing reference matches" />
378 </when> 386 </when>
379 <when value="do_not_set" /> 387 <when value="do_not_set" />
380 </conditional> 388 </conditional>
381 389
382 <!-- reporting --> 390 <!-- reporting -->
647 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> 655 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
648 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/> 656 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
649 <param name="options_type_selector" value="full"/> 657 <param name="options_type_selector" value="full"/>
650 <param name="population_model_selector" value="set"/> 658 <param name="population_model_selector" value="set"/>
651 <param name="P" value="1"/> 659 <param name="P" value="1"/>
660 <param name="trim_complex_tail" value="--trim-complex-tail"/>
652 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" /> 661 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
653 </test> 662 </test>
654 <test> 663 <test>
655 <param name="reference_source_selector" value="history" /> 664 <param name="reference_source_selector" value="history" />
656 <param name="processmode" value="individual" /> 665 <param name="processmode" value="individual" />
678 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/> 687 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
679 <param name="options_type_selector" value="simple"/> 688 <param name="options_type_selector" value="simple"/>
680 <param name="coverage_options_selector" value="set" /> 689 <param name="coverage_options_selector" value="set" />
681 <param name="skip_coverage" value="100" /> 690 <param name="skip_coverage" value="100" />
682 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" /> 691 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
692 </test>
693 <test> <!-- Test with CRAM -->
694 <param name="reference_source_selector" value="history" />
695 <param name="processmode" value="individual" />
696 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
697 <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
698 <param name="options_type_selector" value="simple"/>
699 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
683 </test> 700 </test>
684 </tests> 701 </tests>
685 <help><![CDATA[ 702 <help><![CDATA[
686 **What it does** 703 **What it does**
687 704