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planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
author iuc
date Tue, 02 Apr 2019 17:21:50 -0400
parents 776ebd1239da
children 0aa87d97847f
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2:776ebd1239da 3:feb7e635c6af
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>
38 #end if 38 #end if
39 39
40 #if str( $fastq_input.fastq_input_selector ) == "paired" 40 #if str( $fastq_input.fastq_input_selector ) == "paired"
41 --R1 '$fastq_input.fastq_input1' 41 --R1 '$fastq_input.fastq_input1'
42 --R2 '$fastq_input.fastq_input2' 42 --R2 '$fastq_input.fastq_input2'
43 #end if 43 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
44 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
45 --R1 '$fastq_input.fastq_input.forward' 44 --R1 '$fastq_input.fastq_input.forward'
46 --R2 '$fastq_input.fastq_input.reverse' 45 --R2 '$fastq_input.fastq_input.reverse'
47 #end if 46 #elif str( $fastq_input.fastq_input_selector ) == "single"
48 #if str( $fastq_input.fastq_input_selector ) == "single" 47 --se '$fastq_input.fastq_input_single'
49 --se '$fastq_input.fastq_input' 48 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
50 #end if 49 --peil '$fastq_input.fastq_input_interleaved'
51 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
52 --peil '$fastq_input.fastq_input'
53 #end if 50 #end if
54 51
55 && 52 &&
56 53
57 #import re 54 #import re
58 #if str( $fastq_input.fastq_input_selector ) == "paired" 55 #if str( $fastq_input.fastq_input_selector ) == "paired"
59 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) 56 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
60 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" 57 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
61 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) 58 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
62 #else 59 #elif str( $fastq_input.fastq_input_selector ) == "single"
63 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier) 60 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
61 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
62 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
64 #end if 63 #end if
65 64
66 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && 65 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
67 tar -czf out.tgz ${dir_name} 66 tar -czf out.tgz ${dir_name}
68 #if "outcon" in str($outputs) and $adv.rename_cons 67 #if "outcon" in str($outputs) and $adv.rename_cons
86 <when value="paired"> 85 <when value="paired">
87 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> 86 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
88 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> 87 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
89 </when> 88 </when>
90 <when value="single"> 89 <when value="single">
91 <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> 90 <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
92 </when> 91 </when>
93 <when value="paired_collection"> 92 <when value="paired_collection">
94 <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 93 <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
95 </when> 94 </when>
96 <when value="paired_iv"> 95 <when value="paired_iv">
97 <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 96 <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
98 </when> 97 </when>
99 </conditional> 98 </conditional>
100 99
101 <section name="adv" title="Advanced parameters" expanded="false"> 100 <section name="adv" title="Advanced parameters" expanded="false">
102 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> 101 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
198 <param name="outputs" value="outgff,outsum" /> 197 <param name="outputs" value="outgff,outsum" />
199 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 198 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
200 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> 199 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
201 </test> 200 </test>
202 201
202 <test> <!-- test 3 - fasta ref one snp single -->
203 <param name="ref" value="reference.fasta" ftype="fasta" />
204 <param name="fastq_input_selector" value="single" />
205 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
206 <param name="mincov" value="2" />
207 <param name="minqual" value="60" />
208 <param name="outputs" value="outgff,outsum" />
209 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
210 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
211 </test>
203 </tests> 212 </tests>
204 213
205 214
206 <help><![CDATA[ 215 <help><![CDATA[
207 216