Mercurial > repos > iuc > ivar_variants
comparison ivar_variants.xml @ 6:147465efa99c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
author | iuc |
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date | Thu, 10 Jun 2021 22:06:04 +0000 |
parents | 12d66d0d05ac |
children | 252dfb042563 |
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5:49236b03e4fd | 6:147465efa99c |
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1 <tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy0"> | 1 <tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy1"> |
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> | |
8 </expand> | |
7 <expand macro="version_command" /> | 9 <expand macro="version_command" /> |
8 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '$ref' ref.fa && | 11 ln -s '$ref' ref.fa && |
10 ln -s '$input_bam' sorted.bam && | 12 ln -s '$input_bam' sorted.bam && |
11 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 |
12 -p variants | 14 -p variants |
13 -q $min_qual | 15 -q $min_qual |
14 -t $min_freq | 16 -t $min_freq && |
17 #if str($output_format.choice) == 'vcf' | |
18 python '${__tool_directory__}/ivar_variants_to_vcf.py' | |
19 ${output_format.pass_only} | |
20 variants.tsv '$output_variants' | |
21 #else | |
22 cp variants.tsv '$output_variants' | |
23 #end if | |
15 ]]> </command> | 24 ]]> </command> |
16 <inputs> | 25 <inputs> |
17 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> | 26 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> |
18 <param name="ref" type="data" format="fasta" label="Reference"/> | 27 <param name="ref" type="data" format="fasta" label="Reference"/> |
19 <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/> | 28 <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/> |
20 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> | 29 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> |
30 <conditional name="output_format"> | |
31 <param name="choice" type="select" label="Output format"> | |
32 <option value="tabular">Tabular (native tool output)</option> | |
33 <option value="vcf">VCF</option> | |
34 </param> | |
35 <when value="vcf"> | |
36 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" /> | |
37 </when> | |
38 <when value="tabular" /> | |
39 </conditional> | |
21 </inputs> | 40 </inputs> |
22 <outputs> | 41 <outputs> |
23 <data name="output_variants" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="variants.tsv"/> | 42 <data name="output_variants" format="tabular" label="${tool.name} on ${on_string}"> |
43 <change_format> | |
44 <when input="output_format.choice" value="vcf" format="vcf" /> | |
45 </change_format> | |
46 </data> | |
24 </outputs> | 47 </outputs> |
25 <tests> | 48 <tests> |
26 <test> | 49 <test expect_num_outputs="1"> |
27 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> | 50 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> |
28 <param name="ref" value="zika/db/PRV.fa" /> | 51 <param name="ref" value="zika/db/PRV.fa" /> |
29 <output name="output_variants" file="zika/Z52_a.tsv" lines_diff="10"/> | 52 <output name="output_variants" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> |
53 </test> | |
54 <test expect_num_outputs="1"> | |
55 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> | |
56 <param name="ref" value="zika/db/PRV.fa" /> | |
57 <conditional name="output_format"> | |
58 <param name="choice" value="vcf" /> | |
59 </conditional> | |
60 <output name="output_variants" file="zika/Z52_a.vcf" ftype="vcf"/> | |
30 </test> | 61 </test> |
31 </tests> | 62 </tests> |
32 <help><![CDATA[ | 63 <help><![CDATA[ |
33 iVar uses the output of the samtools mpileup command to call variants - | 64 iVar uses the output of the samtools mpileup command to call variants - |
34 single nucleotide variants(SNVs) and indels. In order to call variants | 65 single nucleotide variants(SNVs) and indels. In order to call variants |
41 at a given position. For insertions, the quality metric is discarded and the | 72 at a given position. For insertions, the quality metric is discarded and the |
42 mpileup depth is used directly. Minimum frequency is the minimum frequency | 73 mpileup depth is used directly. Minimum frequency is the minimum frequency |
43 required for a SNV or indel to be reported. | 74 required for a SNV or indel to be reported. |
44 | 75 |
45 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. | 76 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. |
77 | |
78 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>`_, | |
79 that has been modified to store attributes in INFO fields. | |
46 ]]> </help> | 80 ]]> </help> |
47 <expand macro="citations" /> | 81 <expand macro="citations"> |
82 <citation type="bibtex">@misc{githubivar_variants_to_vcf, | |
83 author = {Fernandez, Sarai Varona and Patel, Harshil}, | |
84 year = {2021}, | |
85 title = {ivar_variants_to_vcf}, | |
86 url = {https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py} | |
87 }</citation> </expand> | |
48 </tool> | 88 </tool> |