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author jpayne
date Wed, 07 Feb 2018 16:37:42 -0500
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1 <tool id="quast-select" name="Select Best" version="0.1.0" profile="16.10">
2 <description>assembly based on a combined QUAST table</description>
3 <requirements>
4 <requirement type="package">python</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #for $asm in $coll
8 ln -s $asm ./$asm.element_identifier &&
9 #end for
10 cp ./\$(python $__tool_directory__/quast_select.py $table $criterion) $output
11 ]]></command>
12 <inputs>
13 <param type="data" format="tsv" name="table" label="Combined QUAST output (from table_union)"/>
14 <param type="select" label="Select best assembly by..." name="criterion">
15 <option value="N50">Longest N50</option>
16 <option value="Largest contig">Longest single contig</option>
17 <option value="# contigs">Fewest contigs</option>
18 <option value="# contigs (>= 1000 bp)">Fewest contigs of length 1kbp or longer</option>
19 <option value="Total length">Total assembly length</option>
20 <option value="Total length (>= 1000 bp)">Total assembly length of contigs longer than 1kbp</option>
21 </param>
22 <param type="data_collection" collection_type="list" format="fasta" name="coll" label="Collection of FASTA assemblies" />
23 </inputs>
24 <outputs>
25 <data format="fasta" name="output" label="Best assembly by ${criterion}" />
26 </outputs>
27 <tests>
28 <test>
29 <param name="table" value="combined_table.tsv" />
30 <param name="coll" >
31 <collection type="list">
32 <element name="sample1" value="sample1.fasta" />
33 <element name="sample2" value="sample2.fasta" />
34 <element name="sample3" value="sample3.fasta" />
35 <element name="sample4" value="sample4.fasta" />
36 </collection>
37 </param>
38 <param name="criterion" value="N50"/>
39 <output name="output" value="sample1.fasta" />
40 </test>
41 </tests>
42 <help><![CDATA[
43 Pick the best assembly from a collection of assemblies and a combined QUAST report.
44 ]]></help>
45 </tool>