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comparison ivar_variants.xml @ 7:252dfb042563 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
author iuc
date Fri, 11 Jun 2021 15:42:14 +0000
parents 147465efa99c
children 38b91a3190cd
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6:147465efa99c 7:252dfb042563
1 <tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy1"> 1 <tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy2">
2 <description>Call variants from aligned BAM file</description> 2 <description>Call variants from aligned BAM file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
11 ln -s '$ref' ref.fa && 11 ln -s '$ref' ref.fa &&
12 ln -s '$input_bam' sorted.bam && 12 ln -s '$input_bam' sorted.bam &&
13 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants 13 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants
14 -p variants 14 -p variants
15 -q $min_qual 15 -q $min_qual
16 -t $min_freq && 16 -t $min_freq
17 #if str($output_format.choice) == 'vcf' 17 #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf"
18 python '${__tool_directory__}/ivar_variants_to_vcf.py' 18 && cp variants.tsv '$output_variants_tabular'
19 #end if
20 #if str($output_format.choice) == 'vcf' or str($output_format.choice) == "tabular_and_vcf"
21 && python '${__tool_directory__}/ivar_variants_to_vcf.py'
19 ${output_format.pass_only} 22 ${output_format.pass_only}
20 variants.tsv '$output_variants' 23 variants.tsv '$output_variants_vcf'
21 #else
22 cp variants.tsv '$output_variants'
23 #end if 24 #end if
24 ]]> </command> 25 ]]> </command>
25 <inputs> 26 <inputs>
26 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> 27 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
27 <param name="ref" type="data" format="fasta" label="Reference"/> 28 <param name="ref" type="data" format="fasta" label="Reference"/>
29 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> 30 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/>
30 <conditional name="output_format"> 31 <conditional name="output_format">
31 <param name="choice" type="select" label="Output format"> 32 <param name="choice" type="select" label="Output format">
32 <option value="tabular">Tabular (native tool output)</option> 33 <option value="tabular">Tabular (native tool output)</option>
33 <option value="vcf">VCF</option> 34 <option value="vcf">VCF</option>
35 <option value="tabular_and_vcf">Both Tabular and VCF</option>
34 </param> 36 </param>
35 <when value="vcf"> 37 <when value="vcf">
38 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" />
39 </when>
40 <when value="tabular_and_vcf">
36 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" /> 41 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" />
37 </when> 42 </when>
38 <when value="tabular" /> 43 <when value="tabular" />
39 </conditional> 44 </conditional>
40 </inputs> 45 </inputs>
41 <outputs> 46 <outputs>
42 <data name="output_variants" format="tabular" label="${tool.name} on ${on_string}"> 47 <data name="output_variants_tabular" format="tabular" label="${tool.name} tabular output on ${on_string}">
43 <change_format> 48 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
44 <when input="output_format.choice" value="vcf" format="vcf" /> 49 <actions>
45 </change_format> 50 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA" />
51 </actions>
52 </data>
53 <data name="output_variants_vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
54 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
46 </data> 55 </data>
47 </outputs> 56 </outputs>
48 <tests> 57 <tests>
49 <test expect_num_outputs="1"> 58 <test expect_num_outputs="1">
50 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> 59 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
51 <param name="ref" value="zika/db/PRV.fa" /> 60 <param name="ref" value="zika/db/PRV.fa" />
52 <output name="output_variants" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> 61 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/>
53 </test> 62 </test>
54 <test expect_num_outputs="1"> 63 <test expect_num_outputs="1">
55 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> 64 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
56 <param name="ref" value="zika/db/PRV.fa" /> 65 <param name="ref" value="zika/db/PRV.fa" />
57 <conditional name="output_format"> 66 <conditional name="output_format">
58 <param name="choice" value="vcf" /> 67 <param name="choice" value="vcf" />
59 </conditional> 68 </conditional>
60 <output name="output_variants" file="zika/Z52_a.vcf" ftype="vcf"/> 69 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/>
61 </test> 70 </test>
71 <test expect_num_outputs="2">
72 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
73 <param name="ref" value="zika/db/PRV.fa" />
74 <conditional name="output_format">
75 <param name="choice" value="tabular_and_vcf" />
76 <param name="pass_only" value="true" />
77 </conditional>
78 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/>
79 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
80 </test>
81
62 </tests> 82 </tests>
63 <help><![CDATA[ 83 <help><![CDATA[
64 iVar uses the output of the samtools mpileup command to call variants - 84 iVar uses the output of the samtools mpileup command to call variants -
65 single nucleotide variants(SNVs) and indels. In order to call variants 85 single nucleotide variants(SNVs) and indels. In order to call variants
66 correctly, the reference file used for alignment must be passed to iVar 86 correctly, the reference file used for alignment must be passed to iVar