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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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18aad692772a planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1 <tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>Identifies amino acid mutations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8
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9 ln -s $input_bam '${input_bam.name}' &&
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10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
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12 quasitools call aavar '${input_bam.name}' $ref_file $input_genes
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14 #if $var_file:
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15 $var_file
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16 #end if
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18 #if $mutation_db:
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19 $mutation_db
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20 #end if
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22 #if $min_freq:
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23 -f $min_freq
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24 #end if
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26 #if $error_rate:
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27 -e $error_rate
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28 #end if
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30 -o output.vcf
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32 ]]></command>
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33 <inputs>
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34 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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35 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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36 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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37 <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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38 <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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39 <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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40 <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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41 </inputs>
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42 <outputs>
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43 <data format="vcf" name="output" from_work_dir="output.vcf" />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input_bam" value="align.bam" />
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48 <param name="ref_file" value="hxb2_pol.fas" />
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49 <param name="var_file" value="nt_variants.vcf" />
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50 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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51 <param name="min_freq" value="0.01" />
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52 <output name="output" >
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53 <assert_contents>
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54 <has_text_matching expression="#CHROM"/>
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55 <has_text_matching expression="0.0779" />
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56 <has_text_matching expression="0.0103;CAT=.;SRVL=." />
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57 <has_text_matching expression="0.0163;CAT=.;SRVL=." />
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58 <has_text_matching expression="0.0148;CAT=.;SRVL=." />
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59 <has_text_matching expression="0.0234;CAT=.;SRVL=." />
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60 <has_text_matching expression="0.0159;CAT=.;SRVL=." />
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61 </assert_contents>
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62 </output>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66
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67 Amino Acid Variants
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68 ===================
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69
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70 Identifies amino acid mutations for a BAM file.
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72
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74 ]]></help>
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75 <expand macro="citations" />
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76 </tool>