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comparison callaavar.xml @ 7:dcd43b402eb3 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author nml
date Fri, 23 Nov 2018 15:43:16 -0500
parents b69e898b8109
children 9def47f3c1e4
comparison
equal deleted inserted replaced
6:9fb9fed71486 7:dcd43b402eb3
1 <tool id="aavariants" name="Amino Acid Variants" version="0.4.2"> 1 <tool id="aavariants" name="Amino Acid Variants" version="0.5.1">
2 <description>Identifies amino acid mutations</description> 2 <description>Identifies amino acid mutations</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.4.2">quasitools</requirement> 4 <requirement type="package" version="0.5.1">quasitools</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9 quasitools call aavar $input_bam $ref_file $var_file $input_genes 9 quasitools call aavar $input_bam $ref_file $input_genes
10
11 #if $var_file:
12 $var_file
13 #end if
10 14
11 #if $mutation_db: 15 #if $mutation_db:
12 $mutation_db 16 $mutation_db
17 #end if
18
19 #if $min_freq:
20 -f $min_freq
21 #end if
22
23 #if $error_rate:
24 -e $error_rate
13 #end if 25 #end if
14 26
15 -o output.vcf 27 -o output.vcf
16 28
17 ]]></command> 29 ]]></command>
18 <inputs> 30 <inputs>
19 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> 31 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
20 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> 32 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
21 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" />
22 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> 33 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
34 <param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
23 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." /> 35 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
24 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." /> 36 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
37 <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
25 </inputs> 38 </inputs>
26 <outputs> 39 <outputs>
27 <data format="vcf" name="output" from_work_dir="output.vcf" /> 40 <data format="vcf" name="output" from_work_dir="output.vcf" />
28 </outputs> 41 </outputs>
29 <tests> 42 <tests>
49 <help><![CDATA[ 62 <help><![CDATA[
50 63
51 Amino Acid Variants 64 Amino Acid Variants
52 =================== 65 ===================
53 66
54 Identifies amino acid mutations. 67 Identifies amino acid mutations for a BAM file.
68
69
55 70
56 ]]></help> 71 ]]></help>
57 <citations> 72 <citations>
73 <citation type="bibtex">
74 @misc{GitHubquasitoolscallaavar,
75 title = {quasitools callaavar},
76 publisher = {phac-nml},
77 journal = {GitHub repository},
78 url = {https://github.com/phac-nml/quasitools},
79 }
80 </citation>
58 </citations> 81 </citations>
59 </tool> 82 </tool>