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comparison ectyper.xml @ 2:d6cf8adc7833 draft

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Added ectyper as a requirement as it should be available via conda
author jpetteng
date Fri, 05 Jan 2018 10:58:39 -0500
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1:2b5e95d690c2 2:d6cf8adc7833
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>