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comparison ecoli_serotyping/ectyper.xml @ 0:7c687720c9e9 draft

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author jpetteng
date Fri, 05 Jan 2018 09:17:33 -0500
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1 <tool id="ectyper" name="ectyper" version="2.0">
2 <requirements>
3 <requirement type="package" version="3.6.3">python</requirement>
4 <requirement type="package">biopython</requirement>
5 <requirement type="package">blast</requirement>
6 <requirement type="package">samtools</requirement>
7 <requirement type="package">bcftools</requirement>
8 <requirement type="package">bowtie</requirement>
9 <requirement type="package">spades</requirement>
10 <requirement type="package">seqtk</requirement>
11 # <requirement type="package">mash</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14
15 ln -s $fasta1 sample_1.fastq;
16 ln -s $fastq2 sample_2.fastq;
17
18 $__tool_directory__/ectyper.py
19 -i ecoliA.fasta for a single file
20 -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files
21 -i ecoli_folder for a folder
22 -i ecoli_folder for a folder
23 -d PERCENTIDENTITY
24 -l PERCENTLENGTH
25 -o OUTPUT;
26 cat SeqSero_result*/Seqsero_result.txt > results.txt;
27
28 ]]></command>
29 <inputs>
30 <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
31 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
32 <param name="numofthr" type="select" label="Number of threads">
33 <option value="1">1</option>
34 <option value="2">2</option>
35 <option value="3">3</option>
36 <option value="4">4</option>
37 </param>
38 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
39 <option value="mem">mem</option>
40 <option value="sam">sam</option>
41 </param>
42
43
44 </inputs>
45 <outputs>
46 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
47 </outputs>
48 <tests>
49 <test>
50 <output name="results" file="results.txt"/>
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 **Usage: ectyper**
56
57 **INPUT**
58
59 Location of new file(s). Can be a single file or a directory
60
61 **PERCENTIDENTITY**
62
63 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
64
65 **PERCENTLENGTH**
66
67 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
68
69 **verify**
70
71 Enable E. Coli. verification
72
73 **species**
74
75 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.
76
77 **OUTPUT**
78 Directory location of output files.
79 ]]></help>
80 </tool>