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annotate aacoverage.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="aacoverage" name="Amino Acid Coverage" version="0.7.0">
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2 <description>Builds an aa census and returns its coverage</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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8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
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10 quasitools aacoverage $input_bam $ref_file $input_genes -o output.csv
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12 ]]></command>
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13 <inputs>
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14 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
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15 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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16 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
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17 </inputs>
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18 <outputs>
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19 <data format="csv" name="output" from_work_dir="output.csv" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input_bam" value="align.bam" />
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24 <param name="ref_file" value="hxb2_pol.fas" />
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25 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
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26 <output name="output" >
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27 <assert_contents>
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28 <has_text text="frame: 0" />
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29 <has_text text="1,0" />
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30 <has_text text="948,1" />
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31 </assert_contents>
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32 </output>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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37 Amino Acid Coverage
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38 ===================
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40 Builds an amino acid census and returns its coverage.
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42 **Output**
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44 A file with one entry per line with the AA position and the coverage at the position.
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46 ]]></help>
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47 <citations>
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48 <citation type="bibtex">
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49 @misc{GitHubquasitoolsaacoverage,
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50 title = {quasitools aacoverage},
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51 publisher = {phac-nml},
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52 journal = {GitHub repository},
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53 url = {https://github.com/phac-nml/quasitools},
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54 }
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55 </citation>
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56 </citations>
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57 </tool>