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annotate callntvar.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="callntvar" name="Nucleotide Variants" version="0.7.0">
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2 <description>Identifies nucleotide variants</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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7
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8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
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9 quasitools call ntvar $input_bam $ref_file
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11 #if $error_rate:
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12 -e $error_rate
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13 #end if
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15 -o output.vcf
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17 ]]></command>
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18 <inputs>
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19 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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20 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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21 <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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22 </inputs>
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23 <outputs>
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24 <data format="vcf" name="output" from_work_dir="output.vcf" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_bam" value="align.bam" ftype="bam" />
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29 <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" />
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30 <output name="output" >
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31 <assert_contents>
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32 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
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33 <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" />
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34 <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" />
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35 <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41
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42 Nucleotide Variants
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43 ===================
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45 Call nucleotide variants for a given BAM file and a supplied reference file.
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47 ]]></help>
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48 <citations>
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49 <citation type="bibtex">
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50 @misc{GitHubquasitoolscallntvar,
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51 title = {quasitools callntvar},
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52 publisher = {phac-nml},
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53 journal = {GitHub repository},
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54 url = {https://github.com/phac-nml/quasitools},
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55 }
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56 </citation>
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57 </citations>
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58 </tool>