|
0
|
1 <tool id="cfsan_snp_pipeline_quast_select" name="CFSAN SNP Pipeline: Select best assembly" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
|
|
|
2 <description>based on a combined QUAST table</description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements"/>
|
|
|
7 <command detect_errors="exit_code"><![CDATA[
|
|
|
8 #for $fasta_file in $input_collection_fasta
|
|
|
9 ln -s $fasta_file $fasta_file.element_identifier &&
|
|
|
10 #end for
|
|
|
11 mv ./\$(python '$__tool_directory__/cfsan_snp_pipeline_quast_select.py' '$input_quast_tsv' '$criterion') '$output'
|
|
|
12 ]]></command>
|
|
|
13 <inputs>
|
|
|
14 <param name="input_quast_tsv" type="data" format="tabular,tsv" label="Combined QUAST output tabular file"/>
|
|
|
15 <param name="criterion" type="select" label="Select best assembly by">
|
|
|
16 <option value="N50" selected="true">longest N50</option>
|
|
|
17 <option value="Largest contig">longest single contig</option>
|
|
|
18 <option value="# contigs">fewest contigs</option>
|
|
|
19 <option value="# contigs (>= 1000 bp)">fewest contigs of length 1kbp or longer</option>
|
|
|
20 <option value="Total length">total assembly length</option>
|
|
|
21 <option value="Total length (>= 1000 bp)">total assembly length of contigs longer than 1kbp</option>
|
|
|
22 </param>
|
|
|
23 <param name="input_collection_fasta" type="data_collection" collection_type="list" format="fasta" label="Collection of FASTA assemblies"/>
|
|
|
24 </inputs>
|
|
|
25 <outputs>
|
|
|
26 <data name="output" format="fasta" label="Best assembly by ${criterion}"/>
|
|
|
27 </outputs>
|
|
|
28 <tests>
|
|
|
29 <test>
|
|
|
30 <param name="input_quast_tsv" value="quast_report.tsv"/>
|
|
|
31 <param name="input_collection_fasta" >
|
|
|
32 <collection type="list">
|
|
|
33 <element name="SRR3168967" value="SRR3168967.fasta"/>
|
|
|
34 </collection>
|
|
|
35 </param>
|
|
|
36 <param name="criterion" value="N50"/>
|
|
|
37 <!-- the output is the same as the input here -->
|
|
|
38 <output name="output" value="SRR3168967.fasta"/>
|
|
|
39 </test>
|
|
|
40 </tests>
|
|
|
41 <help><![CDATA[
|
|
|
42 **What it does**
|
|
|
43
|
|
|
44 Selects the best assembly from a collection of assemblies and a combined QUAST report.
|
|
|
45 ]]></help>
|
|
|
46 <expand macro="citations"/>
|
|
|
47 </tool>
|
|
|
48
|
