annotate callntvar.xml @ 4:8cdffc02d2e2 draft

planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5
author nml
date Wed, 25 Apr 2018 10:38:00 -0400
parents a7093d5933a8
children b69e898b8109
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71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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1 <tool id="callntvar" name="Nucleotide Variants" version="0.1.0">
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2 <description>Identifies nucleotide variants</description>
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3 <requirements>
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8cdffc02d2e2 planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5
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4 <requirement type="package" version="0.3.1">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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9 quasitools call ntvar $input_bam $ref_file
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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11 #if $error_rate:
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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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" />
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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21 <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.01" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.01."/>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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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\s69\sPASS\sDP=157;AC=12;AF=0.0764" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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40 Nucleotide Variants
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41 ===================
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43 Call nucleotide variants for a given BAM file and a supplied reference file.
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44
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45 ]]></help>
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46 <citations>
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47 </citations>
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48 </tool>