Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 1:2b5e95d690c2 draft

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author jpetteng
date Fri, 05 Jan 2018 10:00:07 -0500
parents 7c687720c9e9
children e07f3859a242
comparison
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0:7c687720c9e9 1:2b5e95d690c2
9 <requirement type="package">spades</requirement> 9 <requirement type="package">spades</requirement>
10 <requirement type="package">seqtk</requirement> 10 <requirement type="package">seqtk</requirement>
11 # <requirement type="package">mash</requirement> 11 # <requirement type="package">mash</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 14 #if $jobtype.select == "asm"
15 ln -s $fasta1 sample_1.fastq; 15 ln -s $jobtype.draft sample.fasta;
16 ln -s $fastq2 sample_2.fastq; 16 #else if $jobtype.select == "se"
17 ln -s $jobtype.fastq1 sample_1.fastq;
18 #else if $jobtype.select == "pe"
19 ln -s $jobtype.fastq1 sample_1.fastq;
20 ln -s $jobtype.fastq2 sample_2.fastq;
21 #end if
17 22
18 $__tool_directory__/ectyper.py 23 $__tool_directory__/ectyper.py
19 -i ecoliA.fasta for a single file 24 #if $jobtype.select == "asm"
20 -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files 25 -m 4
21 -i ecoli_folder for a folder 26 -i sample.fasta
22 -i ecoli_folder for a folder 27 #else if $jobtype.select == "se"
23 -d PERCENTIDENTITY 28 -m 3
24 -l PERCENTLENGTH 29 -i sample_1.fastq
25 -o OUTPUT; 30 #else if $jobtype.select == "pe"
31 -m 2
32 -i sample_1.fastq sample_2.fastq
33 #end if
34 -b $maptype.select;
26 cat SeqSero_result*/Seqsero_result.txt > results.txt; 35 cat SeqSero_result*/Seqsero_result.txt > results.txt;
27 36
28 ]]></command> 37 ]]></command>
29 <inputs> 38 <inputs>
30 <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" /> 39 <conditional name="jobtype">
31 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> 40 <param name="select" type="select" label="Assembly or FASTQ Reads?">
32 <param name="numofthr" type="select" label="Number of threads"> 41 <option value="asm">Genome Assembly</option>
33 <option value="1">1</option> 42 <option value="se">Single-End Reads</option>
34 <option value="2">2</option> 43 <option value="pe">Paired-End Reads</option>
35 <option value="3">3</option>
36 <option value="4">4</option>
37 </param> 44 </param>
38 <param name="maptype" type="select" label="Algorithms for BWA mapping?"> 45 <when value="asm">
46 <param name="draft" type="data" format="fasta" label="FASTA" />
47 </when>
48 <when value="se">
49 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
50 </when>
51 <when value="pe">
52 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
53 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
54 </when>
55 </conditional>
56
57 <conditional name="maptype">
58 <param name="select" type="select" label="Algorithms for BWA mapping?">
59 <option value="sam">sam</option>
39 <option value="mem">mem</option> 60 <option value="mem">mem</option>
40 <option value="sam">sam</option>
41 </param> 61 </param>
62 </conditional>
42 63
43 64
44 </inputs> 65 </inputs>
45 <outputs> 66 <outputs>
46 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/> 67 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
54 75
55 **Usage: ectyper** 76 **Usage: ectyper**
56 77
57 **INPUT** 78 **INPUT**
58 79
59 Location of new file(s). Can be a single file or a directory 80 A fasta assembly
60 81
61 **PERCENTIDENTITY** 82 **PERCENTIDENTITY**
62 83
63 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. 84 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
64 85