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planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
author nml
date Mon, 24 Oct 2016 13:15:20 -0400
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1 <tool id="stringmlst" name="StringMLST" version="1.0.4">
2 <description>k-mer tool for multilocus sequence typing</description>
3 <requirements>
4 <requirement type="package" version="2.1">stringmlst</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10
11
12
13 python $__tool_directory__/split_by_allele.py --alleles=$alleles --profiles=$scheme
14 &&
15 stringMLST.py --buildDB -c config.txt -k $kmer -P DB
16
17 &&
18 #if $single_or_paired.type == "single"
19 ln -s "$input_se" "$single_or_paired.input_se.element_identifier".fastq &&
20
21 stringMLST.py
22 --predict
23 -1 "$single_or_paired.input_se.element_identifier".fastq
24 -s
25 #elif $single_or_paired.type == "paired"
26 ln -s "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln -s "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
27 stringMLST.py
28 --predict
29 -1 "$single_or_paired.forward_pe.name"_1.fastq -2 "$single_or_paired.forward_pe.name"_2.fastq
30 -p
31 #else
32 ln -s "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln -s "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
33 stringMLST.py
34 --predict
35 -1 "$single_or_paired.fastq_collection.forward.name"_1.fastq -2 "$single_or_paired.fastq_collection.forward.name"_2.fastq
36 -p
37 #end if
38 -o $output
39 -r
40 -P DB -k $kmer
41
42 ]]></command>
43 <inputs>
44 <conditional name="single_or_paired">
45 <param name="type" type="select" label="Read type">
46 <option value="single">Single-end</option>
47 <option value="paired">Paired-end</option>
48 <option value="collection">Collection Paired-end</option>
49 </param>
50 <when value="single">
51 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
52 </when>
53 <when value="paired">
54 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
55 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
56 </when>
57 <when value="collection">
58 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
59 </when>
60 </conditional>
61 <param name="kmer" type="integer" label="K-mer to use" value="35" help=" Kmer length for which the db was created(Default k = 35)." />
62 <param name="scheme" type="data" format="tabular" label="ST definitions for MLST scheme"/>
63 <param name="alleles" type="data" format="fasta" label="Fasta file of MLST alleles"/>
64
65 </inputs>
66 <outputs>
67 <data format="tabular" name="output" label="Results"/>
68 <data format="txt" name="log" label="Log" from_work_dir="DB.log"/>
69 <data format="fastqsanger" name="reads" label='Reads' from_work_dir="*.fq" >
70
71 </data>
72 </outputs>
73 <tests>
74 <test>
75 <param name="scheme" value="st.tabular" />
76 <param name="alleles" value="st.fasta" />
77 <param name="input_se" value="input.fastqsanger" />
78 <output file="results.tsv" ftype="tabular" name="output" />
79 </test>
80 </tests>
81 <help><![CDATA[
82 Original manual for command line available at http://jordan.biology.gatech.edu/page/software/stringmlst/stringMLST-useageDocumentation.pdf
83 ]]>
84
85 </help>
86 <citations>
87 </citations>
88 </tool>