Mercurial > repos > iuc > snippy

annotate snippy.xml @ 0:ff177a01b5ca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
author iuc
date Fri, 16 Feb 2018 13:39:50 -0500
parents
children d4e6df2bc5e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
1 <tool id="snippy" name="snippy" version="@VERSION@">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
2 <description>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
4 </description>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
5 <macros>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
6 <import>macros.xml</import>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
7 </macros>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
8 <expand macro="requirements" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
9 <expand macro="version_command" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
10
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
12
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
13 #if $ref.is_of_type("fasta")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
14 cp '$ref' 'foo.fna' &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
15 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
16 #if $ref.is_of_type("genbank")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
17 cp '$ref' 'foo.gbk' &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
18 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
19 snippy
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
20 --outdir 'out'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
21 --cpus "\${GALAXY_SLOTS:-1}"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
22 #if $ref.is_of_type("fasta")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
23 --ref 'foo.fna'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
24 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
25 #if $ref.is_of_type("genbank")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
26 --ref 'foo.gbk'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
27 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
28 --mapqual $adv.mapqual
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
29 --mincov $adv.mincov
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
30 --minfrac $adv.minfrac
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
31 #if $adv.rgid
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
32 --rgid '$advanced.rgid'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
33 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
34 #if $adv.bwaopt
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
35 --bwaopt '$advanced.bwaopt'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
36 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
37
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
38 #if str( $fastq_input.fastq_input_selector ) == "paired"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
39 --pe1 '$fastq_input.fastq_input1'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
40 --pe2 '$fastq_input.fastq_input2'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
41 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
42 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
43 --pe1 '$fastq_input.fastq_input1.forward'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
44 --pe2 '$fastq_input.fastq_input1.reverse'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
45 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
46 #if str( $fastq_input.fastq_input_selector ) == "single"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
47 --se '$fastq_input.fastq_input1'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
48 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
49 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
50 --peil '$fastq_input.fastq_input1'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
51 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
52
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
53 &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
54
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
55 gunzip out/snps.depth.gz
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
56
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
57 &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
58
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
59 #import re
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
60 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
61 mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
62
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
63 tar -czf out.tgz ${dir_name}
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
64
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
66 ]]></command>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
68 <inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
69
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
70 <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
72 <conditional name="fastq_input">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
73 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
74 <option value="paired">Paired</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
75 <option value="single">Single</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
76 <option value="paired_collection">Paired Collection</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
77 <option value="paired_iv">Paired Interleaved</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
78 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
79 <when value="paired">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
80 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
81 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
82 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
83 <when value="single">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
84 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
85 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
86 <when value="paired_collection">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
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"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
88 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
89 <when value="paired_iv">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
90 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
91 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
92 </conditional>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
93
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
94 <section name="adv" title="Advanced parameters" expanded="false">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
95 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
96 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
97 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
98 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
99 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
100 </section>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
101
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
102 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
103 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
104 <option value="outgff" selected="False">The variants in GFF3 format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
105 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
106 <option value="outsum" selected="False">A summary of the samples and mapping</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
107 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
108 <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
109 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
110 <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
111 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
112 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
113 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
114
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
115 </inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
116
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
117 <outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
118
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
119 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
120 <filter>outputs and 'outvcf' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
121 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
122 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
123 <filter>outputs and 'outgff' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
124 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
125 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
126 <filter>outputs and 'outtab' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
127 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
128 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
129 <filter>outputs and 'outsum' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
130 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
131 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
132 <filter>outputs and 'outlog' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
133 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
134 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
135 <filter>outputs and 'outaln' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
136 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
137 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
138 <filter>outputs and 'outcon' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
139 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
140 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
141 <filter>outputs and 'outdep' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
142 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
143 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
144 <filter>outputs and 'outbam' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
145 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
146 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
147 <filter>outputs and 'outzip' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
148 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
149
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
150 </outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
151
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
152 <tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
153
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
154 <test> <!-- test 1 - fasta ref default -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
155 <param name="ref" value="wildtype.fna" ftype="fasta" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
156 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
157 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
158 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
159 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
160 <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
161 <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
162 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
163
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
164 <test> <!-- test 2 - gbk ref default -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
165 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
166 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
167 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
168 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
169 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
170 <output name="snpsum" ftype="tabular" file="gbk_ref/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
171 <output name="snpgff" ftype="gff3" file="gbk_ref/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
172 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
173
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
174 <test> <!-- test 3 - gbk mapqual=40 -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
175 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
176 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
177 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
178 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
179 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
180 <param name="mapqual" value="40" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
181 <output name="snpsum" ftype="tabular" file="map_qual/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
182 <output name="snpgff" ftype="gff3" file="map_qual/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
183 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
184
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
185 <test> <!-- test 4 - gbk mincov=15 -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
186 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
187 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
188 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
189 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
190 <param name="mincov" value="15" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
191 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
192 <output name="snpsum" ftype="tabular" file="min_cov/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
193 <output name="snpgff" ftype="gff3" file="min_cov/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
194 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
195
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
196 <test> <!-- test 5 - gbk minfrac=0.7 -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
197 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
198 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
199 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
200 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
201 <param name="minfrac" value="0.7" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
202 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
203 <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
204 <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
205 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
206
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
207 </tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
208
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
209
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
210 <help><![CDATA[
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
211
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
212 **Snippy @VERSION@**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
213
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
214 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
215
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
216 **Author**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
217
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
218 Torsten Seemann
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
219
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
220 **Inputs**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
221
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
222 - NGS Reads in fastq format (single or paired end)
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
223 - Reference file in either fasta or genbank format
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
224
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
225 If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
226
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
227 **Advanced options**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
228
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
229 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
230
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
231 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
232
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
233 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
234
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
235 - rgid - String - Use this @RG ID: in the BAM header (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
236
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
237 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
238
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
239 **Further information**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
240
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
241 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
242
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
243 ]]></help>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
244 <expand macro="citations"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
245
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
246 </tool>