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annotate complexity_bam.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
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9def47f3c1e4 planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
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1 <tool id="complexity_bam" name="Complexity BAM" version="0.7.0">
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2 <requirements>
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3 <requirement type="package" version="0.7.0">quasitools</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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7 ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' &&
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9 quasitools complexity bam '$ref_file' '$input_bam' $k -f '$filter_size' -o output.csv
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11 ]]></command>
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12 <inputs>
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13 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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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="k" type="integer" label="k-mer size" value="0" min="0" />
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16 <param name="filter_size" type="integer" label="Filter size" value="0" min="0" />
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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="ref_file" value="generated.fasta" />
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24 <param name="input_bam" value="generated.bam" />
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25 <param name="k" value="200" />
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26 <param name="filter_size" value="0" />
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27 <output name="output" >
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28 <assert_contents>
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29 <has_text text="Position" />
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30 <has_text text="0" />
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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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36 <help><![CDATA[
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37 Quasispecies Complexity
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38 =======================
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40 Calculates various quasispecies complexity measures on next generation sequenced data from a BAM file and it's corresponding reference file.
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41
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42 The measures of complexity are taken from the following work:
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43 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
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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{GitHubquasitoolscomplexity,
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50 title = {quasitools complexity},
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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>