Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 34:3853eaea6e00 draft default tip

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author jpetteng
date Tue, 09 Jan 2018 11:36:07 -0500
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33:cad63e627e0a 34:3853eaea6e00
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>