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annotate callcodonvar.xml @ 8:9def47f3c1e4 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author nml
date Tue, 06 Aug 2019 08:50:28 -0400
parents dcd43b402eb3
children 18aad692772a
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9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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1 <tool id="callcodonvar" name="Codon Variants" version="0.7.0">
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2 <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.0">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 cat $input_genes &&
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10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
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11 quasitools call codonvar $input_bam $ref_file $offset $input_genes
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13 #if $var_file:
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14 $var_file
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15 #end if
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16
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17 #if $error_rate:
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18 -e $error_rate
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19 #end if
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21 -o output.csv
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23 ]]></command>
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24 <inputs>
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25 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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26 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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27 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
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28 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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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." />
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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." />
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31 </inputs>
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32 <outputs>
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33 <data format="csv" name="output" from_work_dir="output.csv" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input_bam" value="align.bam" />
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38 <param name="ref_file" value="hxb2_pol.fas" />
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39 <param name="offset" value="1269"/>
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40 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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41 <output name="output" >
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42 <assert_contents>
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43 <has_text text="#gene,nt position (gene),nt start position,nt end position,ref codon,mutant codon,ref AA,mutant AA,coverage,mutant frequency,mutant type,NS count,S count" />
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44 <has_text text="RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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51 Codon Variants
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52 ==============
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53
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54 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
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55 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
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56 a synonymous or non-synonymous mutation.
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57
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58 ]]></help>
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59 <citations>
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60 <citation type="bibtex">
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61 @misc{GitHubquasitoolscallcodonvar,
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62 title = {quasitools callcodonvar},
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63 publisher = {phac-nml},
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64 journal = {GitHub repository},
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65 url = {https://github.com/phac-nml/quasitools},
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66 }
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67 </citation>
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68 </citations>
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69 </tool>