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1 <tool id="quast-select" name="Select Best" version="0.1.0" profile="16.10">
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2 <description>assembly based on a combined QUAST table</description>
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3 <requirements>
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4 <requirement type="package">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #for $asm in $coll
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8 ln -s $asm ./$asm.element_identifier &&
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9 #end for
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10 cp ./\$(python $__tool_directory__/quast_select.py $table $criterion) $output
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11 ]]></command>
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12 <inputs>
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13 <param type="data" format="tsv" name="table" label="Combined QUAST output (from table_union)"/>
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14 <param type="select" label="Select best assembly by..." name="criterion">
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15 <option value="N50">Longest N50</option>
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16 <option value="Largest contig">Longest single contig</option>
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17 <option value="# contigs">Fewest contigs</option>
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18 <option value="# contigs (>= 1000 bp)">Fewest contigs of length 1kbp or longer</option>
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19 <option value="Total length">Total assembly length</option>
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20 <option value="Total length (>= 1000 bp)">Total assembly length of contigs longer than 1kbp</option>
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21 </param>
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22 <param type="data_collection" collection_type="list" format="fasta" name="coll" label="Collection of FASTA assemblies" />
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23 </inputs>
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24 <outputs>
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25 <data format="fasta" name="output" label="Best assembly by ${criterion}" />
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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="table" value="combined_table.tsv" />
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30 <param name="coll" >
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31 <collection type="list">
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32 <element name="sample1" value="sample1.fasta" />
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33 <element name="sample2" value="sample2.fasta" />
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34 <element name="sample3" value="sample3.fasta" />
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35 <element name="sample4" value="sample4.fasta" />
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36 </collection>
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37 </param>
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38 <param name="criterion" value="N50"/>
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39 <output name="output" value="sample1.fasta" />
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 Pick the best assembly from a collection of assemblies and a combined QUAST report.
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44 ]]></help>
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45 </tool> |
