Mercurial > repos > youyuh48 > kraken_tools

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author youyuh48
date Sun, 02 May 2021 06:21:24 +0000
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1 <tool id="extract_kraken_reads" name="extract_kraken_reads" version="0.1.0">
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2 <description>Extract reads classified at any user-specified taxonomy IDs.</description>
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3 <requirements>
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4 <requirement type="package" version="1.2">krakentools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 extract_kraken_reads.py
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9 -k '$classification'
5ca43a5fac32 planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/KrakenTools
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10 -s '$seq'
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11 -t $taxid
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12 --max $maxreads
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13 -o '$output1'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param type="data" name="classification" format="tabular" label="Kraken classification output" />
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18 <param type="data" name="seq" format="fasta,fastq" label="Select the same fasta/fastq reads used" />
5ca43a5fac32 planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/KrakenTools
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19 <param type="text" name="taxid" label="Taxonomy ID[s] of reads to extract (space-delimited)" />
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20 <param name="maxreads" type="integer" value="10" min="1" label="Maximum number of reads to save" />
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21 </inputs>
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22 <outputs>
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23 <data name="output1" format="fasta" label="${tool.name} on ${on_string}" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="classification" value="kraken2_class.tsv" />
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28 <param name="seq" value="tid1613.fasta" />
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29 <param name="taxid" value="1613" />
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30 <param name="taxid" value="1" />
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31 <output name="output1" file="out.fasta" />
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32 </test>
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33 </tests>
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34 <help>
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35 <![CDATA[
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36 .. class:: infomark
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37
5ca43a5fac32 planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/KrakenTools
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38 **What it does**
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39
5ca43a5fac32 planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/KrakenTools
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40 This program extract reads classified at any user-specified taxonomy IDs. User must specify the Kraken output file, the sequence file(s), and at least one taxonomy ID.
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41
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42 As of April 19, 2021, this script is compatible with KrakenUniq/Kraken2Uniq reports.
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43 ]]>
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44 </help>
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45 <citations>
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46 <citation type="bibtex">
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47 @misc{githubKrakenTools,
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48 title = {KrakenTools},
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49 publisher = {GitHub},
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50 journal = {GitHub repository},
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51 url = {https://github.com/jenniferlu717/KrakenTools},
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52 }</citation>
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53 </citations>
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54 </tool>