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comparison ivar_variants.xml @ 11:38b91a3190cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
author iuc
date Wed, 11 Jan 2023 09:53:09 +0000
parents 252dfb042563
children ed28dd32141c
comparison
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10:584beffa972b 11:38b91a3190cd
1 <tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy2"> 1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
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"/>
7 <requirement type="package" version="3">python</requirement> 7 <expand macro="version_command"/>
8 </expand>
9 <expand macro="version_command" />
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 ln -s '$ref' ref.fa && 9 ln -s '$ref' ref.fa &&
12 ln -s '$input_bam' sorted.bam && 10 ln -s '$input_bam' sorted.bam &&
13 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants 11 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants
14 -p variants 12 -p variants
15 -q $min_qual 13 -q $min_qual
16 -t $min_freq 14 -t $min_freq
17 #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf" 15 #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf"
18 && cp variants.tsv '$output_variants_tabular' 16 #if str($gtf) != 'None':
17 -r ref.fa
18 -g '$gtf'
19 #end if
19 #end if 20 #end if
20 #if str($output_format.choice) == 'vcf' or str($output_format.choice) == "tabular_and_vcf" 21 #if str($output_format.choice) == "vcf" or str($output_format.choice) == "tabular_and_vcf"
21 && python '${__tool_directory__}/ivar_variants_to_vcf.py' 22 && python '${__tool_directory__}/ivar_variants_to_vcf.py'
22 ${output_format.pass_only} 23 ${output_format.pass_only}
23 variants.tsv '$output_variants_vcf' 24 variants.tsv variants.vcf
24 #end if 25 #end if
25 ]]> </command> 26 ]]></command>
26 <inputs> 27 <inputs>
27 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> 28 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
28 <param name="ref" type="data" format="fasta" label="Reference"/> 29 <param name="ref" type="data" format="fasta" label="Reference"/>
29 <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/> 30 <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/>
30 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> 31 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/>
33 <option value="tabular">Tabular (native tool output)</option> 34 <option value="tabular">Tabular (native tool output)</option>
34 <option value="vcf">VCF</option> 35 <option value="vcf">VCF</option>
35 <option value="tabular_and_vcf">Both Tabular and VCF</option> 36 <option value="tabular_and_vcf">Both Tabular and VCF</option>
36 </param> 37 </param>
37 <when value="vcf"> 38 <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 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/>
39 </when> 40 </when>
40 <when value="tabular_and_vcf"> 41 <when value="tabular_and_vcf">
41 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" /> 42 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/>
43 <param name="gtf" argument="-g" optional="true" type="data" format="gff" label="Coordinates of ORFs for optional variant effect prediction" help="Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level. This has no effect on the VCF output."/>
42 </when> 44 </when>
43 <when value="tabular" /> 45 <when value="tabular">
44 </conditional> 46 <param name="gtf" argument="-g" optional="true" type="data" format="gff" label="Coordinates of ORFs for optional variant effect prediction" help="Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level."/>
47 </when>
48 </conditional>
45 </inputs> 49 </inputs>
46 <outputs> 50 <outputs>
47 <data name="output_variants_tabular" format="tabular" label="${tool.name} tabular output on ${on_string}"> 51 <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
48 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter> 52 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
49 <actions> 53 <actions>
50 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA" /> 54 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA"/>
51 </actions> 55 </actions>
52 </data> 56 </data>
53 <data name="output_variants_vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> 57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
54 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> 58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
55 </data> 59 </data>
56 </outputs> 60 </outputs>
57 <tests> 61 <tests>
58 <test expect_num_outputs="1"> 62 <test expect_num_outputs="1">
59 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> 63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
60 <param name="ref" value="zika/db/PRV.fa" /> 64 <param name="ref" value="zika/db/PRV.fa"/>
61 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> 65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/>
62 </test> 66 </test>
63 <test expect_num_outputs="1"> 67 <test expect_num_outputs="1">
64 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> 68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
65 <param name="ref" value="zika/db/PRV.fa" /> 69 <param name="ref" value="zika/db/PRV.fa"/>
66 <conditional name="output_format"> 70 <conditional name="output_format">
67 <param name="choice" value="vcf" /> 71 <param name="choice" value="vcf"/>
68 </conditional> 72 </conditional>
69 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/> 73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/>
70 </test> 74 </test>
71 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2">
72 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> 76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
73 <param name="ref" value="zika/db/PRV.fa" /> 77 <param name="ref" value="zika/db/PRV.fa"/>
74 <conditional name="output_format"> 78 <conditional name="output_format">
75 <param name="choice" value="tabular_and_vcf" /> 79 <param name="choice" value="tabular_and_vcf"/>
76 <param name="pass_only" value="true" /> 80 <param name="pass_only" value="true"/>
77 </conditional> 81 </conditional>
78 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> 82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/>
79 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> 83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
80 </test> 84 </test>
81 85 <test expect_num_outputs="1">
86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
87 <param name="ref" value="zika/db/PRV.fa"/>
88 <param name="gtf" value="zika/db/PRV.gff"/>
89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
90 </test>
91 <test expect_num_outputs="2">
92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
93 <param name="ref" value="zika/db/PRV.fa"/>
94 <param name="gtf" value="zika/db/PRV.gff"/>
95 <conditional name="output_format">
96 <param name="choice" value="tabular_and_vcf"/>
97 <param name="pass_only" value="true"/>
98 </conditional>
99 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
100 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
101 </test>
82 </tests> 102 </tests>
83 <help><![CDATA[ 103 <help><![CDATA[
84 iVar uses the output of the samtools mpileup command to call variants - 104 iVar uses the output of the samtools mpileup command to call variants -
85 single nucleotide variants(SNVs) and indels. In order to call variants 105 single nucleotide variants(SNVs) and indels. In order to call variants
86 correctly, the reference file used for alignment must be passed to iVar 106 correctly, the reference file used for alignment must be passed to iVar
87 using the -r flag. The output of samtools pileup is piped into ivar variants 107 using the -r flag. The output of samtools pileup is piped into ivar variants
88 to generate a .tsv file with the variants. There are two parameters that can 108 to generate a .tsv file with the variants. There are two parameters that can
89 be set for variant calling using iVar - minimum quality(Default: 20) and 109 be set for variant calling using iVar - minimum quality(Default: 20) and
90 minimum frequency(Default: 0.03). Minimum quality is the minimum quality for 110 minimum frequency(Default: 0.03). Minimum quality is the minimum quality for
91 a base to be counted towards the ungapped depth to canculate iSNV frequency 111 a base to be counted towards the ungapped depth to canculate iSNV frequency
92 at a given position. For insertions, the quality metric is discarded and the 112 at a given position. For insertions, the quality metric is discarded and the
93 mpileup depth is used directly. Minimum frequency is the minimum frequency 113 mpileup depth is used directly. Minimum frequency is the minimum frequency
94 required for a SNV or indel to be reported. 114 required for a SNV or indel to be reported.
95
96 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
97 115
98 Optionally output is converted to VCF using a version of the `ivar_variants_to_vcf.py script <https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py>`_, 116 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
99 that has been modified to store attributes in INFO fields. 117
100 ]]> </help> 118 Optionally output is converted to VCF using a version of the
119 `ivar_variants_to_vcf.py script <https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py>`_,
120 that has been modified to store attributes in INFO fields.
121 ]]></help>
101 <expand macro="citations"> 122 <expand macro="citations">
102 <citation type="bibtex">@misc{githubivar_variants_to_vcf, 123 <citation type="bibtex">@misc{githubivar_variants_to_vcf,
103 author = {Fernandez, Sarai Varona and Patel, Harshil}, 124 author = {Fernandez, Sarai Varona and Patel, Harshil},
104 year = {2021}, 125 year = {2021},
105 title = {ivar_variants_to_vcf}, 126 title = {ivar_variants_to_vcf},
106 url = {https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py} 127 url = {https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py}
107 }</citation> </expand> 128 }</citation>
129 </expand>
108 </tool> 130 </tool>