Mercurial > repos > jpetteng > ectyper
comparison ecoli_serotyping/ectyper.xml @ 34:3853eaea6e00 draft default tip
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author | jpetteng |
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date | Tue, 09 Jan 2018 11:36:07 -0500 |
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33:cad63e627e0a | 34:3853eaea6e00 |
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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">ectyper</requirement> | |
5 <requirement type="package">biopython</requirement> | |
6 <requirement type="package">blast</requirement> | |
7 <requirement type="package">samtools</requirement> | |
8 <requirement type="package">bcftools</requirement> | |
9 <requirement type="package">bowtie</requirement> | |
10 <requirement type="package">spades</requirement> | |
11 <requirement type="package">seqtk</requirement> | |
12 <requirement type="package">pandas</requirement> | |
13 <requirement type="package">mash</requirement> | |
14 </requirements> | |
15 <command detect_errors="exit_code"><![CDATA[ | |
16 #if $jobtype.select == "asm" | |
17 ln -s $jobtype.draft sample.fasta; | |
18 #else if $jobtype.select == "se" | |
19 ln -s $jobtype.fastq1 sample_1.fastq; | |
20 #else if $jobtype.select == "pe" | |
21 ln -s $jobtype.fastq1 sample_1.fastq; | |
22 ln -s $jobtype.fastq2 sample_2.fastq; | |
23 #end if | |
24 | |
25 python $__tool_directory__/bin/ectyper | |
26 #if $jobtype.select == "asm" | |
27 -m 4 | |
28 -i sample.fasta | |
29 #else if $jobtype.select == "se" | |
30 -m 3 | |
31 -i sample_1.fastq | |
32 #else if $jobtype.select == "pe" | |
33 -m 2 | |
34 -i sample_1.fastq sample_2.fastq | |
35 #end if | |
36 -b $maptype.select; | |
37 cat ectyper_result*/ectyper_result.txt > results.txt; | |
38 | |
39 ]]></command> | |
40 <inputs> | |
41 <conditional name="jobtype"> | |
42 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
43 <option value="asm">Genome Assembly</option> | |
44 <option value="se">Single-End Reads</option> | |
45 <option value="pe">Paired-End Reads</option> | |
46 </param> | |
47 <when value="asm"> | |
48 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
49 </when> | |
50 <when value="se"> | |
51 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
52 </when> | |
53 <when value="pe"> | |
54 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
55 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> | |
56 </when> | |
57 </conditional> | |
58 | |
59 <conditional name="maptype"> | |
60 <param name="select" type="select" label="Algorithms for BWA mapping?"> | |
61 <option value="sam">sam</option> | |
62 <option value="mem">mem</option> | |
63 </param> | |
64 </conditional> | |
65 | |
66 | |
67 </inputs> | |
68 <outputs> | |
69 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/> | |
70 </outputs> | |
71 <tests> | |
72 <test> | |
73 <output name="results" file="results.txt"/> | |
74 </test> | |
75 </tests> | |
76 <help><![CDATA[ | |
77 | |
78 **Usage: ectyper** | |
79 | |
80 **INPUT** | |
81 | |
82 A fasta assembly | |
83 | |
84 **PERCENTIDENTITY** | |
85 | |
86 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. | |
87 | |
88 **PERCENTLENGTH** | |
89 | |
90 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. | |
91 | |
92 **verify** | |
93 | |
94 Enable E. Coli. verification | |
95 | |
96 **species** | |
97 | |
98 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time. | |
99 | |
100 **OUTPUT** | |
101 Directory location of output files. | |
102 ]]></help> | |
103 </tool> |