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1 <tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
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4
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="3.7.0">python</requirement>
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5 <requirement type="package" version="1.72">biopython</requirement>
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6 </requirements>
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7
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8 <command>
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9 mkdir outputs;
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10 python3 $__tool_directory__/demultiplex.py
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11 --input $input
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12 --format auto
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13 --output-dir ./outputs
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14 --mapping-file $mapping
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15 </command>
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16 <inputs>
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17 <param name="input" type="data" format='fasta,fastq' label="The input fasta/fastq"/>
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18 <param name="mapping" type="data" format='tabular' label="The mapping file"/>
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19 </inputs>
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20 <outputs>
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21 <!--<data name="debug" format="txt" label="debug"/>-->
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22 <collection name='demultiplex_out' format_source='input' type="list">
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23 <discover_datasets pattern="__designation_and_ext__" directory="outputs"/>
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24 <!--<discover_datasets pattern="(?P<designation>.+)\.(?P<ext>.+)" directory="outputs"/>-->
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25 </collection>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="input.fastq"/>
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30 <param name="mapping" value="mapping.txt"/>
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31 <output_collection name="demultiplex_out" type="list">
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32 <element name="sequence1" file="sequence1.fastq"/>
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33 <element name="sequence2" file="sequence2.fastq"/>
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34 </output_collection>
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35 </test>
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36 <test>
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37 <param name="input" value="input.fasta"/>
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38 <param name="mapping" value="mapping.txt"/>
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39 <output_collection name="demultiplex_out" type="list">
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40 <element name="sequence1" file="sequence1.fasta"/>
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41 <element name="sequence2" file="sequence2.fasta"/>
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42 </output_collection>
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43 </test>
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44 </tests>
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45 <help>
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46 There is no help
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47 </help>
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48 <citations>
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49 <citation type="bibtex">@misc{Demultplex-EMC,
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50 author = {Erasmus MC},
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51 title = {Demultiplex-EMC},
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52 year = {2018},
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53 howpublished = {https://github.com/ErasmusMC-Bioinformatics/Demultiplex}
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54 }</citation>
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55 </citations>
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56 </tool>
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