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comparison callcodonvar.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="callcodonvar" name="Codon Variants" version="0.4.2"> 1 <tool id="callcodonvar" name="Codon Variants" version="0.5.1">
2 <description>Identifies codon variants and non-synonymous/synonymous mutations</description> 2 <description>Identifies codon variants and non-synonymous/synonymous 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 cat $input_genes && 8 cat $input_genes &&
9 9
10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
11 quasitools call codonvar $input_bam $ref_file $offset $input_genes 11 quasitools call codonvar $input_bam $ref_file $offset $input_genes
12
13 #if $var_file:
14 $var_file
15 #end if
12 16
13 #if $error_rate: 17 #if $error_rate:
14 -e $error_rate 18 -e $error_rate
15 #end if 19 #end if
16 20
20 <inputs> 24 <inputs>
21 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> 25 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
22 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> 26 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
23 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> 27 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
24 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> 28 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
25 <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.01" help="Estimated sequencing error rate. Defaults to 0.01." /> 29 <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021." />
30 <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." />
26 </inputs> 31 </inputs>
27 <outputs> 32 <outputs>
28 <data format="csv" name="output" from_work_dir="output.csv" /> 33 <data format="csv" name="output" from_work_dir="output.csv" />
29 </outputs> 34 </outputs>
30 <tests> 35 <tests>
50 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to 55 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
51 a synonymous or non-synonymous mutation. 56 a synonymous or non-synonymous mutation.
52 57
53 ]]></help> 58 ]]></help>
54 <citations> 59 <citations>
60 <citation type="bibtex">
61 @misc{GitHubquasitoolscallcodonvar,
62 title = {quasitools callcodonvar},
63 publisher = {phac-nml},
64 journal = {GitHub repository},
65 url = {https://github.com/phac-nml/quasitools},
66 }
67 </citation>
55 </citations> 68 </citations>
56 </tool> 69 </tool>