Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 2:15572bf93a2a

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planemo upload
author jpayne
date Fri, 09 Nov 2018 16:02:31 -0500
parents fae43708974d
children b18e8cdfdf81
comparison
equal deleted inserted replaced
1:fae43708974d 2:15572bf93a2a
9 <requirement type="package" version="0.7.17">bwa</requirement> 9 <requirement type="package" version="0.7.17">bwa</requirement>
10 <requirement type="package" version="3.12.0">spades</requirement> 10 <requirement type="package" version="3.12.0">spades</requirement>
11 <requirement type="package" version="2.27.1">bedtools</requirement> 11 <requirement type="package" version="2.27.1">bedtools</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 #if $reads.reads_select == 'history' 14 #if $reads.reads_select == 'history':
15 #set name = $reads.forward.name.split('.')[0].replace(' ','_') 15 #set name = $reads.forward.name.split('.')[0].replace(' ','_')
16 #set forward = $reads.forward 16 #set forward = $reads.forward
17 #set reverse = $reads.reverse 17 #set reverse = $reads.reverse
18 #else 18 #else
19 #set name = $reads.coll.name.replace(' ', '_') 19 #set name = $reads.coll.name.replace(' ', '_')
20 #set forward = $reads.coll.forward 20 #set forward = $reads.coll.forward
21 #set reverse = $reads.coll.reverse 21 #set reverse = $reads.coll.reverse
22 #end if 22 #end if
23 echo $name ; 23 echo $name ;
24 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz') 24 echo "-=-=-=-=-" ;
25 gunzip -c $forward > forward.fastq; 25 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
26 gunzip -c $forward > forward.fastq;
26 #set forward = './forward.fastq' 27 #set forward = './forward.fastq'
27 #end if 28 #end if
28 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz') 29 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz'):
29 gunzip -c $reverse > reverse.fastq; 30 gunzip -c $reverse > reverse.fastq;
30 #set reverse = './reverse.fastq' 31 #set reverse = './reverse.fastq'
31 #end if 32 #end if
32 ln -s forward.fastq ${name}_1.fastq; 33 ln -s forward.fastq ${name}_1.fastq;
33 ln -s reverse.fastq ${name}_2.fastq; 34 ln -s reverse.fastq ${name}_2.fastq;
34 mkdir ./output; 35 mkdir ./output;
35 python $__tool_directory__/SeqSero2/SeqSero2_package.py 36 python $__tool_directory__/SeqSero2/SeqSero2_package.py
36 -p \${GALAXY_SLOTS:-4} 37 -p \${GALAXY_SLOTS:-4}
37 -t 2 38 -t 2
38 -m $mode 39 -m $mode
39 -d ./output 40 -d ./output
40 -b $maptype 41 #if $mode == 'a':
41 -i ${name}_1.fastq ${name}_2.fastq && 42 -b $maptype
42 echo "-=-=-=-=-" && 43 #end if
43 cat output/SeqSero_log.txt && 44 -i ${name}_1.fastq ${name}_2.fastq &&
44 echo "-=-=-=-=-" && 45 echo "-=-=-=-=-" &&
45 ls -lah ./output 46 cat output/SeqSero_log.txt &&
47 echo "-=-=-=-=-" &&
48 ls -lah ./output
46 ]]></command> 49 ]]></command>
47 <inputs> 50 <inputs>
48
49 <param label="Analysis mode" type="select" name="mode">
50 <option value="k">k-mer mode</option>
51 <option value="a">allele mode</option>
52 </param>
53 51
54 <conditional name="reads"> 52 <conditional name="reads">
55 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 53 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
56 <option value="collection">Paired collection from your history</option> 54 <option value="collection">Paired collection from your history</option>
57 <option value="history">Two FASTQ datasets from your history</option> 55 <option value="history">Two FASTQ datasets from your history</option>
71 <option value="1">1</option> 69 <option value="1">1</option>
72 <option value="2">2</option> 70 <option value="2">2</option>
73 <option value="3">3</option> 71 <option value="3">3</option>
74 <option value="4">4</option> --> 72 <option value="4">4</option> -->
75 <!-- </param> --> 73 <!-- </param> -->
76 <param name="maptype" type="select" label="Algorithms for BWA mapping?"> 74
75 <param label="Analysis mode" type="select" name="mode">
76 <option value="k">k-mer mode</option>
77 <option value="a">allele mode</option>
78 </param>
79
80 <param name="maptype" type="select" label="Algorithms for BWA mapping">
77 <option value="mem">mem</option> 81 <option value="mem">mem</option>
78 <option value="sam">sam</option> 82 <option value="sam">sam</option>
79 </param> 83 </param>
84
80 85
81 86
82 </inputs> 87 </inputs>
83 <outputs> 88 <outputs>
84 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/> 89 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>