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comparison snippy.xml @ 1:82f2b6f20fa2 draft

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planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
author iuc
date Sat, 26 Jan 2019 14:36:48 -0500
parents c9a8ef2aa380
children 776ebd1239da
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0:c9a8ef2aa380 1:82f2b6f20fa2
1 <tool id="snippy" name="snippy" version="@VERSION@"> 1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
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 #if str( $fastq_input.fastq_input_selector ) == "paired" 38 #if str( $fastq_input.fastq_input_selector ) == "paired"
39 --pe1 '$fastq_input.fastq_input1' 39 --pe1 '$fastq_input.fastq_input1'
40 --pe2 '$fastq_input.fastq_input2' 40 --pe2 '$fastq_input.fastq_input2'
41 #end if 41 #end if
42 #if str( $fastq_input.fastq_input_selector ) == "paired_collection" 42 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
43 --pe1 '$fastq_input.fastq_input1.forward' 43 --pe1 '$fastq_input.fastq_input.forward'
44 --pe2 '$fastq_input.fastq_input1.reverse' 44 --pe2 '$fastq_input.fastq_input.reverse'
45 #end if 45 #end if
46 #if str( $fastq_input.fastq_input_selector ) == "single" 46 #if str( $fastq_input.fastq_input_selector ) == "single"
47 --se '$fastq_input.fastq_input1' 47 --se '$fastq_input.fastq_input'
48 #end if 48 #end if
49 #if str( $fastq_input.fastq_input_selector ) == "paired_iv" 49 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
50 --peil '$fastq_input.fastq_input1' 50 --peil '$fastq_input.fastq_input'
51 #end if 51 #end if
52 52
53 && 53 &&
54 54
55 gunzip out/snps.depth.gz 55 gunzip out/snps.depth.gz
56 56
57 && 57 &&
58 58
59 #import re 59 #import re
60 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) 60 #if str( $fastq_input.fastq_input_selector ) == "paired"
61 mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ && 61 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
62 62 #else
63 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
64 #end if
65
66 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&
63 tar -czf out.tgz ${dir_name} 67 tar -czf out.tgz ${dir_name}
64 68
65 69
66 ]]></command> 70 ]]></command>
67 71
79 <when value="paired"> 83 <when value="paired">
80 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> 84 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
81 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> 85 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
82 </when> 86 </when>
83 <when value="single"> 87 <when value="single">
84 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> 88 <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
85 </when> 89 </when>
86 <when value="paired_collection"> 90 <when value="paired_collection">
87 <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 91 <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"/>
88 </when> 92 </when>
89 <when value="paired_iv"> 93 <when value="paired_iv">
90 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 94 <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
91 </when> 95 </when>
92 </conditional> 96 </conditional>
93 97
94 <section name="adv" title="Advanced parameters" expanded="false"> 98 <section name="adv" title="Advanced parameters" expanded="false">
95 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> 99 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
202 <param name="outputs" value="outgff,outsum" /> 206 <param name="outputs" value="outgff,outsum" />
203 <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" /> 207 <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" />
204 <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" /> 208 <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
205 </test> 209 </test>
206 210
211 <test> <!-- test 6 - fasta ref default paired_collection -->
212 <param name="ref" value="wildtype.fna" ftype="fasta" />
213 <param name="fastq_input_selector" value="paired_collection" />
214 <param name="fastq_input">
215 <collection type="paired">
216 <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
217 <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
218 </collection>
219 </param>
220 <param name="outputs" value="outgff,outsum" />
221 <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
222 <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
223 </test>
224
207 </tests> 225 </tests>
208 226
209 227
210 <help><![CDATA[ 228 <help><![CDATA[
211 229