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comparison ectyper.xml @ 0:4724d20b14de draft

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author jpetteng
date Wed, 10 Jan 2018 14:20:54 -0500
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1 <tool id="ectyper" name="ectyper" version="0.1">
2 <requirements>
3 <requirement type="package" version="0.1">ectyper</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 #if $jobtype.select == "asm"
7 ln -s $jobtype.draft sample.fasta;
8 #else if $jobtype.select == "se"
9 ln -s $jobtype.fastq1 sample_1.fastq;
10 #else if $jobtype.select == "pe"
11 ln -s $jobtype.fastq1 sample_1.fastq;
12 ln -s $jobtype.fastq2 sample_2.fastq;
13 #end if
14
15 $__tool_directory__/ectyper
16 #if $jobtype.select == "asm"
17 -i sample.fasta
18 #else if $jobtype.select == "se"
19 -i sample_1.fastq
20 #else if $jobtype.select == "pe"
21 -i sample_1.fastq sample_2.fastq
22 #end if
23 -d $percent_identity
24 -l $percent_length
25 -o "./"; cat ./output/output.csv > results.csv;
26
27 ]]></command>
28 <inputs>
29 <conditional name="jobtype">
30 <param name="select" type="select" label="Assembly or FASTQ Reads?">
31 <option value="asm">Genome Assembly</option>
32 <option value="se">Single-End Reads</option>
33 <option value="pe">Paired-End Reads</option>
34 </param>
35 <when value="asm">
36 <param name="draft" type="data" format="fasta" label="FASTA" />
37 </when>
38 <when value="se">
39 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
40 </when>
41 <when value="pe">
42 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
43 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
44 </when>
45 </conditional>
46
47 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
48 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
49
50 </inputs>
51 <outputs>
52 <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
53 </outputs>
54
55 <help><![CDATA[
56
57 **Usage: ectyper**
58
59 **INPUT**
60
61 A fasta assembly or single or paired end reads
62
63 **PERCENTIDENTITY**
64
65 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
66
67 **PERCENTLENGTH**
68
69 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
70
71 https://github.com/phac-nml/ecoli_serotyping
72
73 ]]></help>
74 </tool>