Mercurial > repos > iuc > ivar_variants
annotate ivar_variants.xml @ 15:045d6d00f606 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
author | iuc |
---|---|
date | Tue, 27 Jun 2023 17:13:41 +0000 |
parents | ed28dd32141c |
children |
rev | line source |
---|---|
15
045d6d00f606
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents:
12
diff
changeset
|
1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
2 <description>Call variants from aligned BAM file</description> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
3 <macros> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
5 </macros> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
6 <expand macro="requirements"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
7 <expand macro="version_command"/> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
9 ln -s '$ref' ref.fa && |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
10 ln -s '$input_bam' sorted.bam && |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
11 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
12 -p variants |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
13 -q $min_qual |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
14 -t $min_freq |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
15 #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf" |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
16 #if str($gtf) != 'None': |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
17 -r ref.fa |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
18 -g '$gtf' |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
19 #end if |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
20 #end if |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
21 #if str($output_format.choice) == "vcf" or str($output_format.choice) == "tabular_and_vcf" |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
22 && python '${__tool_directory__}/ivar_variants_to_vcf.py' |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
23 ${output_format.pass_only} |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
24 variants.tsv variants.vcf |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
25 #end if |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
26 ]]></command> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
27 <inputs> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
28 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
29 <param name="ref" type="data" format="fasta" label="Reference"/> |
12
ed28dd32141c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
iuc
parents:
11
diff
changeset
|
30 <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
31 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
32 <conditional name="output_format"> |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
33 <param name="choice" type="select" label="Output format"> |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
34 <option value="tabular">Tabular (native tool output)</option> |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
35 <option value="vcf">VCF</option> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
36 <option value="tabular_and_vcf">Both Tabular and VCF</option> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
37 </param> |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
38 <when value="vcf"> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
39 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
40 </when> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
41 <when value="tabular_and_vcf"> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
42 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
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."/> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
44 </when> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
45 <when value="tabular"> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
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."/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
47 </when> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
48 </conditional> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
49 </inputs> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
50 <outputs> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
51 <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}"> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
52 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter> |
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
53 <actions> |
12
ed28dd32141c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
iuc
parents:
11
diff
changeset
|
54 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA,POS_AA"/> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
55 </actions> |
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
56 </data> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
59 </data> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
60 </outputs> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
61 <tests> |
15
045d6d00f606
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents:
12
diff
changeset
|
62 <test expect_num_outputs="1"> <!-- test 1 --> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
64 <param name="ref" value="zika/db/PRV.fa"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
66 </test> |
15
045d6d00f606
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents:
12
diff
changeset
|
67 <test expect_num_outputs="1"> <!-- test 2 --> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
69 <param name="ref" value="zika/db/PRV.fa"/> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
70 <conditional name="output_format"> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
71 <param name="choice" value="vcf"/> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
72 </conditional> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
74 </test> |
15
045d6d00f606
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents:
12
diff
changeset
|
75 <test expect_num_outputs="2"> <!-- test 3 --> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
77 <param name="ref" value="zika/db/PRV.fa"/> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
78 <conditional name="output_format"> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
79 <param name="choice" value="tabular_and_vcf"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
80 <param name="pass_only" value="true"/> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
81 </conditional> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/> |
7
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> |
252dfb042563
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
6
diff
changeset
|
84 </test> |
15
045d6d00f606
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents:
12
diff
changeset
|
85 <test expect_num_outputs="1"> <!-- test 4 --> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
87 <param name="ref" value="zika/db/PRV.fa"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
88 <param name="gtf" value="zika/db/PRV.gff"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
90 </test> |
15
045d6d00f606
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents:
12
diff
changeset
|
91 <test expect_num_outputs="2"> <!-- test 5 --> |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
93 <param name="ref" value="zika/db/PRV.fa"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
94 <param name="gtf" value="zika/db/PRV.gff"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
95 <conditional name="output_format"> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
96 <param name="choice" value="tabular_and_vcf"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
97 <param name="pass_only" value="true"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
98 </conditional> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
99 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
100 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
101 </test> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
102 </tests> |
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
103 <help><![CDATA[ |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
104 iVar uses the output of the samtools mpileup command to call variants - |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
105 single nucleotide variants(SNVs) and indels. In order to call variants |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
106 correctly, the reference file used for alignment must be passed to iVar |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
107 using the -r flag. The output of samtools pileup is piped into ivar variants |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
108 to generate a .tsv file with the variants. There are two parameters that can |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
109 be set for variant calling using iVar - minimum quality(Default: 20) and |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
110 minimum frequency(Default: 0.03). Minimum quality is the minimum quality for |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
111 a base to be counted towards the ungapped depth to canculate iSNV frequency |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
112 at a given position. For insertions, the quality metric is discarded and the |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
113 mpileup depth is used directly. Minimum frequency is the minimum frequency |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
114 required for a SNV or indel to be reported. |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
115 |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
116 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
117 |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
118 Optionally output is converted to VCF using a version of the |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
119 `ivar_variants_to_vcf.py script <https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py>`_, |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
120 that has been modified to store attributes in INFO fields. |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
121 ]]></help> |
6
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
122 <expand macro="citations"> |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
123 <citation type="bibtex">@misc{githubivar_variants_to_vcf, |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
124 author = {Fernandez, Sarai Varona and Patel, Harshil}, |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
125 year = {2021}, |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
126 title = {ivar_variants_to_vcf}, |
147465efa99c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
parents:
0
diff
changeset
|
127 url = {https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py} |
11
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
128 }</citation> |
38b91a3190cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
iuc
parents:
7
diff
changeset
|
129 </expand> |
0
12d66d0d05ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff
changeset
|
130 </tool> |