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annotate callcodonvar.xml @ 6:9fb9fed71486 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
author nml
date Fri, 12 Oct 2018 09:16:03 -0400
parents b69e898b8109
children dcd43b402eb3
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b69e898b8109 planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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1 <tool id="callcodonvar" name="Codon Variants" version="0.4.2">
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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="0.4.2">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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b69e898b8109 planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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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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b69e898b8109 planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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11 quasitools call codonvar $input_bam $ref_file $offset $input_genes
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13 #if $error_rate:
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b69e898b8109 planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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14 -e $error_rate
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15 #end if
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17 -o output.csv
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19 ]]></command>
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20 <inputs>
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21 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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22 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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23 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
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24 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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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." />
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26 </inputs>
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27 <outputs>
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28 <data format="csv" name="output" from_work_dir="output.csv" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_bam" value="align.bam" />
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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33 <param name="ref_file" value="hxb2_pol.fas" />
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34 <param name="offset" value="1269"/>
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35 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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36 <output name="output" >
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37 <assert_contents>
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38 <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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39 <has_text text="RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000" />
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40 </assert_contents>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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46 Codon Variants
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47 ==============
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48
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49 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
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50 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
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51 a synonymous or non-synonymous mutation.
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53 ]]></help>
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54 <citations>
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55 </citations>
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56 </tool>