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comparison cfsan_snp_pipeline_quast_select.xml @ 0:fedc60909fbe draft default tip

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author greg
date Tue, 17 Oct 2023 14:13:45 +0000
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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