Mercurial > repos > nml > vcf2snvalignment
comparison vcf2snvalignment.xml @ 0:7d66bf698382 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
author | nml |
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date | Tue, 27 Aug 2019 12:33:24 -0400 |
parents | |
children | d2096d0c149e |
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1 <tool id="vcf2snvalignment" name="VCF 2 snvalignment" version ="1.8.2"> | |
2 <description>create a snv alignment from multiple merged VCF files</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 | |
8 | |
9 #for $f in $vcf_collection.keys# | |
10 #set $name = str($vcf_collection[$f]).split('/')[-1] | |
11 ln -f -s '$vcf_collection[$f]' && | |
12 | |
13 #if $vcf_collection[$f].metadata.bcf_index: | |
14 ln -s '${$vcf_collection[$f].metadata.bcf_index}' ${name}.csi && | |
15 #else | |
16 bcftools index $name && | |
17 #end if | |
18 #end for# | |
19 | |
20 vcf2snv_alignment.pl | |
21 | |
22 -r "$reference" | |
23 #if str($invalid) != 'None': | |
24 --invalid-pos "$invalid" | |
25 #end if | |
26 -f fasta | |
27 -f phylip | |
28 --numcpus \${GALAXY_SLOTS:-2} | |
29 --fasta "$ref_fasta" | |
30 | |
31 #for $f in $vcf_collection.keys# | |
32 #set $path = str($vcf_collection[$f]).split('/')[-1] | |
33 --consolidate_vcf "$f=$path" | |
34 #end for# | |
35 | |
36 #if $strain_list.select_list == "include": | |
37 --include '$strain_list.include' | |
38 #elif $strain_list.select_list == "exclude": | |
39 --exclude '$strain_list.exclude' | |
40 #end if | |
41 | |
42 ##mark where the output files will be sent to, simply have to match them up later in the xml output section | |
43 -o 'snvalign' | |
44 ]]> | |
45 </command> | |
46 <inputs> | |
47 <param name="reference" type="text" label="Reference Name" value='reference' /> | |
48 <param name="ref_fasta" type="data" label="Reference Fasta File" format="fasta"/> | |
49 <param name="invalid" type="data" label="Invalid position file" format="gff,bed" optional="true"/> | |
50 <conditional name="strain_list"> | |
51 <param name="select_list" type="select" label="Strain Selecting options"> | |
52 <option value="all">Use all strains in collection</option> | |
53 <option value="include">Provide list of subset of strains to only include</option> | |
54 <option value="exclude">Provide list of subset of strains to exclude</option> | |
55 </param> | |
56 <when value="include"> | |
57 <param name="include" type="data" label="List of strains to be include" format="text" optional="false"/> | |
58 </when> | |
59 <when value="exclude"> | |
60 <param name="exclude" type="data" label="List of strains to be excluded" format="text" optional="false"/> | |
61 </when> | |
62 <when value="all"/> | |
63 </conditional> | |
64 <param name="vcf_collection" type="data_collection" label="Combined VCF Files" help="" optional="false" format="bcf,bcf_bgzip" collection_type="list" /> | |
65 </inputs> | |
66 <outputs> | |
67 <data format="tabular" name="positions" from_work_dir="snvalign-positions.tsv" /> | |
68 <data format="fasta" name="fasta" from_work_dir="snvalign.fasta"/> | |
69 <data format="phylip" name="phylip" from_work_dir="snvalign.phy" /> | |
70 <data format="tabular" name="vcf2core" from_work_dir="snvalign-stats.csv" /> | |
71 </outputs> | |
72 <tests> | |
73 <test> | |
74 <param name="reference" value="ref"/> | |
75 <param name="ref_fasta" value="reference.fasta"/> | |
76 <param name="vcf_collection"> | |
77 <collection type="list"> | |
78 <element name="v1" value="consolidate_vcf/v1.bcf.gz"/> | |
79 <element name="v2" value="consolidate_vcf/v2.bcf.gz"/> | |
80 </collection> | |
81 </param> | |
82 <output name="positions" file="expected_positions.tsv"/> | |
83 <output name="fasta" file="expected_fasta.fasta"/> | |
84 <output name="phylip" file="expected_phylip.phy"/> | |
85 <output name="vcf2core" file="expected_stats.csv"/> | |
86 </test> | |
87 </tests> | |
88 | |
89 <help> | |
90 Produces an alignment of SNVs from the merged variant/non-variant calls produced from the "consolidate_vcfs" tool. | |
91 </help> | |
92 | |
93 <citations> | |
94 </citations> | |
95 | |
96 </tool> |