Mercurial > repos > jpetteng > ectyper
comparison ectyper.xml @ 2:d6cf8adc7833 draft
Added ectyper as a requirement as it should be available via conda
author | jpetteng |
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date | Fri, 05 Jan 2018 10:58:39 -0500 |
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1:2b5e95d690c2 | 2:d6cf8adc7833 |
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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">mash</requirement> | |
13 </requirements> | |
14 <command detect_errors="exit_code"><![CDATA[ | |
15 #if $jobtype.select == "asm" | |
16 ln -s $jobtype.draft sample.fasta; | |
17 #else if $jobtype.select == "se" | |
18 ln -s $jobtype.fastq1 sample_1.fastq; | |
19 #else if $jobtype.select == "pe" | |
20 ln -s $jobtype.fastq1 sample_1.fastq; | |
21 ln -s $jobtype.fastq2 sample_2.fastq; | |
22 #end if | |
23 | |
24 $__tool_directory__/ectyper.py | |
25 #if $jobtype.select == "asm" | |
26 -m 4 | |
27 -i sample.fasta | |
28 #else if $jobtype.select == "se" | |
29 -m 3 | |
30 -i sample_1.fastq | |
31 #else if $jobtype.select == "pe" | |
32 -m 2 | |
33 -i sample_1.fastq sample_2.fastq | |
34 #end if | |
35 -b $maptype.select; | |
36 cat ectyper_result*/ectyper_result.txt > results.txt; | |
37 | |
38 ]]></command> | |
39 <inputs> | |
40 <conditional name="jobtype"> | |
41 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
42 <option value="asm">Genome Assembly</option> | |
43 <option value="se">Single-End Reads</option> | |
44 <option value="pe">Paired-End Reads</option> | |
45 </param> | |
46 <when value="asm"> | |
47 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
48 </when> | |
49 <when value="se"> | |
50 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
51 </when> | |
52 <when value="pe"> | |
53 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
54 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> | |
55 </when> | |
56 </conditional> | |
57 | |
58 <conditional name="maptype"> | |
59 <param name="select" type="select" label="Algorithms for BWA mapping?"> | |
60 <option value="sam">sam</option> | |
61 <option value="mem">mem</option> | |
62 </param> | |
63 </conditional> | |
64 | |
65 | |
66 </inputs> | |
67 <outputs> | |
68 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/> | |
69 </outputs> | |
70 <tests> | |
71 <test> | |
72 <output name="results" file="results.txt"/> | |
73 </test> | |
74 </tests> | |
75 <help><![CDATA[ | |
76 | |
77 **Usage: ectyper** | |
78 | |
79 **INPUT** | |
80 | |
81 A fasta assembly | |
82 | |
83 **PERCENTIDENTITY** | |
84 | |
85 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. | |
86 | |
87 **PERCENTLENGTH** | |
88 | |
89 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. | |
90 | |
91 **verify** | |
92 | |
93 Enable E. Coli. verification | |
94 | |
95 **species** | |
96 | |
97 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time. | |
98 | |
99 **OUTPUT** | |
100 Directory location of output files. | |
101 ]]></help> | |
102 </tool> |