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annotate 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
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1 <tool id="aavariants" name="Amino Acid Variants" version="0.5.1">
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2 <description>Identifies amino acid mutations</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.1">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7
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8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
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9 quasitools call aavar $input_bam $ref_file $input_genes
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11 #if $var_file:
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12 $var_file
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13 #end if
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15 #if $mutation_db:
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16 $mutation_db
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17 #end if
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19 #if $min_freq:
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20 -f $min_freq
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21 #end if
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23 #if $error_rate:
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24 -e $error_rate
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25 #end if
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27 -o output.vcf
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29 ]]></command>
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30 <inputs>
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31 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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32 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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33 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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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." />
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35 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
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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." />
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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."/>
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38 </inputs>
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39 <outputs>
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40 <data format="vcf" name="output" from_work_dir="output.vcf" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_bam" value="align.bam" />
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45 <param name="ref_file" value="hxb2_pol.fas" />
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46 <param name="var_file" value="nt_variants.vcf" />
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47 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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48 <param name="min_freq" value="0.01" />
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49 <output name="output" >
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50 <assert_contents>
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51 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
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52 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." />
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53 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." />
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54 <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." />
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55 <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." />
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56 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." />
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57 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63
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64 Amino Acid Variants
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65 ===================
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66
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67 Identifies amino acid mutations for a BAM file.
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68
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69
0
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70
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71 ]]></help>
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72 <citations>
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73 <citation type="bibtex">
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74 @misc{GitHubquasitoolscallaavar,
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75 title = {quasitools callaavar},
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76 publisher = {phac-nml},
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77 journal = {GitHub repository},
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78 url = {https://github.com/phac-nml/quasitools},
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79 }
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80 </citation>
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81 </citations>
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82 </tool>