Mercurial > repos > iuc > snippy

comparison snippy.xml @ 9:e4d0231d8595 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
author iuc
date Mon, 27 Jan 2020 21:50:49 -0500
parents 32f2211eeec3
children 5bbf9eada9c2
comparison
equal deleted inserted replaced
8:32f2211eeec3 9:e4d0231d8595
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1"> 1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy2">
2 <description> 2 <description>
3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
10 10
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 12
13 @REFERENCE_SOURCE_FILE@ 13 @REFERENCE_SOURCE_FILE@
14 14
15 #import re
16 #if str( $fastq_input.fastq_input_selector ) == "paired"
17 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
20 #elif str( $fastq_input.fastq_input_selector ) == "single"
21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
22 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
23 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
24 #end if
25
15 snippy 26 snippy
16 --outdir 'out' 27 --outdir '${dir_name}'
17 --cpus \${GALAXY_SLOTS:-1} 28 --cpus \${GALAXY_SLOTS:-1}
18 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024)) 29 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
19 @REFERENCE_COMMAND@ 30 @REFERENCE_COMMAND@
20 --mapqual $adv.mapqual 31 --mapqual $adv.mapqual
21 --mincov $adv.mincov 32 --mincov $adv.mincov
38 --se '$fastq_input.fastq_input_single' 49 --se '$fastq_input.fastq_input_single'
39 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" 50 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
40 --peil '$fastq_input.fastq_input_interleaved' 51 --peil '$fastq_input.fastq_input_interleaved'
41 #end if 52 #end if
42 53
43 && 54 #if "outcon" in str($outputs) and $adv.rename_cons
44 55 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
45 #import re
46 #if str( $fastq_input.fastq_input_selector ) == "paired"
47 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
48 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
49 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
50 #elif str( $fastq_input.fastq_input_selector ) == "single"
51 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
53 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
54 #end if 56 #end if
55 57
56 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && 58 && cp -r '${dir_name}' out
57 tar -czf out.tgz ${dir_name} 59 && tar -czf out.tgz '${dir_name}'
58 #if "outcon" in str($outputs) and $adv.rename_cons
59 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
60 #end if
61
62
63 ]]> </command> 60 ]]> </command>
64 61
65 <inputs> 62 <inputs>
66 <expand macro="reference_selector" /> 63 <expand macro="reference_selector" />
67 <conditional name="fastq_input"> 64 <conditional name="fastq_input">