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1 <tool id="kwip" name="kwip" version="1.1.7">
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7
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2 <description>Calculates k-mer weighted inner product, a de novo estimator of genetic similarity</description>
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3 <requirements>
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4 <requirement type="package" version="0.2.0">kwip</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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7 #for $input in $inputs# cp $input $(basename "$input.element_identifier" .fastq).ct.gz && #end for#
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8 kwip
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9 -t $advanced.thread
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10 -k kwip.kernel
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11 -d kwip.dist
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12 $advanced.unweighted
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13 #for $input in $inputs# $(basename "$input.element_identifier" .fastq).ct.gz #end for#
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14 #for $input in $inputs# && rm $(basename "$input.element_identifier" .fastq).ct.gz #end for#
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15 ]]></command>
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16 <inputs>
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17 <param name="inputs" format="data" type="data_collection" label="inputs" help="Specify dataset with hashed reads"/>
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18 <section name="advanced" title="Advanced options" expanded="false">
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19 <param type="boolean" argument="--unweighted" label="Unweighted Inner Product" checked="false" truevalue="--unweighted" falsevalue="" help="Use the unweighted inner proudct kernel. (default: False)"/>
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20 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
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21
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22 </section>
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23 </inputs>
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24 <outputs>
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25 <data name="kwip_kernel" label="kWip kernel" format="txt" type="data" from_work_dir="kwip.kernel"/>
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26 <data name="kwip_distance" label="kWip distance" format="txt" type="data" from_work_dir="kwip.dist"/>
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27 </outputs>
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28 <tests>
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29 </tests>
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30 <help><![CDATA[
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31 usage: USAGE: kwip [options] hashes
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32
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33 kWip Options.
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34
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35 optional arguments:
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36 -t, --threads Number of threads to utilise. [default N_CPUS]
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37 -k, --kernel Output file for the kernel matrix. [default None]
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38 -d, --distance Output file for the distance matrix. [default stdout]
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39 -U, --unweighted Use the unweighted inner proudct kernel. [default off]
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40 -w, --weights Bin weight vector file (input, or output w/ -C).
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41 -C, --calc-weights Calculate only the bin weight vector, not kernel matrix.
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42 -h, --help Print this help message.
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43 -V, --version Print the version string.
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44 -v, --verbose Increase verbosity. May or may not acutally do anything.
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45 -q, --quiet Execute silently but for errors.
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46
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47 Each sample's oxli Countgraph should be specified after arguments:
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48 kwip [options] sample1.ct sample2.ct ... sampleN.ct
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49
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50 ]]></help>
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51 <citations>
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52 <citation type="bibtex">
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53 @misc{githubPythonPRINCE,
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54 author = {Murray, Kevin},
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55 year = {2015},
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56 title = {kWIP},
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57 publisher = {GitHub},
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58 journal = {GitHub repository},
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59 url = {https://github.com/kdmurray91/kWIPE},
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60 }</citation>
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61 </citations>
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62 </tool>
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