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1 <tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="3.7.0">python</requirement>
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4 <requirement type="package" version="1.72">biopython</requirement>
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5 </requirements>
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6 <description></description>
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7 <command>
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8 mkdir outputs;
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9 python3 $__tool_directory__/demultiplex.py
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10 --input $input
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11 --format auto
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12 --output-dir ./outputs
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13 --mapping-file $mapping
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14 </command>
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15 <inputs>
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16 <param name="input" type="data" format='fasta,fastq' label="The input fasta/fastq"/>
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17 <param name="mapping" type="data" format='tabular' label="The mapping file"/>
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18 </inputs>
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19 <outputs>
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20 <data name="debug" format="txt" label="debug"/>
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21 <collection name='demultiplex_out' format_source='input' type='list'>
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22 <discover_datasets pattern="__name_and_ext__" directory="outputs" format_source='input'/>
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23 </collection>
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24 </outputs>
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25 <tests>
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26 <!--
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27 <test>
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28 <param name="input1" value="1.bed"/>
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29 <param name="input2" value="2.bed"/>
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30 <output name="out_file1" file="cat_wrapper_out1.bed"/>
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31 </test>
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32 TODO: if possible, enhance the underlying test code to handle this test
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33 the problem is multiple params with the same name "input2"
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34 <test>
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35 <param name="input1" value="1.bed"/>
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36 <param name="input2" value="2.bed"/>
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37 <param name="input2" value="3.bed"/>
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38 <output name="out_file1" file="cat_wrapper_out2.bed"/>
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39 </test>
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40 -->
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41 </tests>
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42 <help>
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43 There is no help
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44 </help>
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45 </tool>
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46
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