Mercurial > repos > iuc > snippy

annotate snippy.xml @ 1:82f2b6f20fa2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
author iuc
date Sat, 26 Jan 2019 14:36:48 -0500
parents c9a8ef2aa380
children 776ebd1239da
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
2 <description>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
4 </description>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
5 <macros>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
6 <import>macros.xml</import>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
7 </macros>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
8 <expand macro="requirements" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
9 <expand macro="version_command" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
10
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
12
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
13 #if $ref.is_of_type("fasta")
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
14 cp '$ref' 'foo.fna' &&
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
15 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
16 #if $ref.is_of_type("genbank")
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
17 cp '$ref' 'foo.gbk' &&
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
18 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
19 snippy
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
20 --outdir 'out'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
21 --cpus "\${GALAXY_SLOTS:-1}"
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
22 #if $ref.is_of_type("fasta")
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
23 --ref 'foo.fna'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
24 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
25 #if $ref.is_of_type("genbank")
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
26 --ref 'foo.gbk'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
27 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
28 --mapqual $adv.mapqual
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
29 --mincov $adv.mincov
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
30 --minfrac $adv.minfrac
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
31 #if $adv.rgid
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
32 --rgid '$advanced.rgid'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
33 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
34 #if $adv.bwaopt
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
35 --bwaopt '$advanced.bwaopt'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
36 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
37
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
38 #if str( $fastq_input.fastq_input_selector ) == "paired"
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
39 --pe1 '$fastq_input.fastq_input1'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
40 --pe2 '$fastq_input.fastq_input2'
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
41 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
42 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
43 --pe1 '$fastq_input.fastq_input.forward'
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
44 --pe2 '$fastq_input.fastq_input.reverse'
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
45 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
46 #if str( $fastq_input.fastq_input_selector ) == "single"
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
47 --se '$fastq_input.fastq_input'
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
48 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
49 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
50 --peil '$fastq_input.fastq_input'
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
51 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
52
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
53 &&
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
54
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
55 gunzip out/snps.depth.gz
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
56
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
57 &&
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
58
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
59 #import re
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
60 #if str( $fastq_input.fastq_input_selector ) == "paired"
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
61 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
62 #else
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
63 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
64 #end if
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
66 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67 tar -czf out.tgz ${dir_name}
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
68
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
69
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
70 ]]></command>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
72 <inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
73
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
74 <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" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
75
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
76 <conditional name="fastq_input">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
77 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
78 <option value="paired">Paired</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
79 <option value="single">Single</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
80 <option value="paired_collection">Paired Collection</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
81 <option value="paired_iv">Paired Interleaved</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
82 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
83 <when value="paired">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
84 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
85 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
86 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
87 <when value="single">
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
88 <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
89 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
90 <when value="paired_collection">
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
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"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
92 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
93 <when value="paired_iv">
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
94 <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
95 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
96 </conditional>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
97
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
98 <section name="adv" title="Advanced parameters" expanded="false">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
99 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
100 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
101 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
102 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
103 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
104 </section>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
105
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
106 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
107 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
108 <option value="outgff" selected="False">The variants in GFF3 format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
109 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
110 <option value="outsum" selected="False">A summary of the samples and mapping</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
111 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
112 <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>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
113 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
114 <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
115 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
116 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
117 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
118
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
119 </inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
120
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
121 <outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
122
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
123 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
124 <filter>outputs and 'outvcf' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
125 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
126 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
127 <filter>outputs and 'outgff' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
128 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
129 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
130 <filter>outputs and 'outtab' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
131 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
132 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
133 <filter>outputs and 'outsum' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
134 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
135 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
136 <filter>outputs and 'outlog' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
137 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
138 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
139 <filter>outputs and 'outaln' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
140 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
141 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
142 <filter>outputs and 'outcon' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
143 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
144 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
145 <filter>outputs and 'outdep' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
146 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
147 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
148 <filter>outputs and 'outbam' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
149 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
150 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
151 <filter>outputs and 'outzip' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
152 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
153
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
154 </outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
155
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
156 <tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
157
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
158 <test> <!-- test 1 - fasta ref default -->
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
159 <param name="ref" value="wildtype.fna" ftype="fasta" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
160 <param name="fastq_input_selector" value="paired" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
161 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
162 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
163 <param name="outputs" value="outgff,outsum" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
164 <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
165 <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
166 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
167
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
168 <test> <!-- test 2 - gbk ref default -->
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
169 <param name="ref" value="wildtype.gbk" ftype="genbank" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
170 <param name="fastq_input_selector" value="paired" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
171 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
172 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
173 <param name="outputs" value="outgff,outsum" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
174 <output name="snpsum" ftype="tabular" file="gbk_ref/snps.txt" lines_diff="6" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
175 <output name="snpgff" ftype="gff3" file="gbk_ref/snps.gff" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
176 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
177
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
178 <test> <!-- test 3 - gbk mapqual=40 -->
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
179 <param name="ref" value="wildtype.gbk" ftype="genbank" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
180 <param name="fastq_input_selector" value="paired" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
181 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
182 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
183 <param name="outputs" value="outgff,outsum" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
184 <param name="mapqual" value="40" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
185 <output name="snpsum" ftype="tabular" file="map_qual/snps.txt" lines_diff="6" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
186 <output name="snpgff" ftype="gff3" file="map_qual/snps.gff" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
187 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
188
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
189 <test> <!-- test 4 - gbk mincov=15 -->
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
190 <param name="ref" value="wildtype.gbk" ftype="genbank" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
191 <param name="fastq_input_selector" value="paired" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
192 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
193 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
194 <param name="mincov" value="15" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
195 <param name="outputs" value="outgff,outsum" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
196 <output name="snpsum" ftype="tabular" file="min_cov/snps.txt" lines_diff="6" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
197 <output name="snpgff" ftype="gff3" file="min_cov/snps.gff" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
198 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
199
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
200 <test> <!-- test 5 - gbk minfrac=0.7 -->
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
201 <param name="ref" value="wildtype.gbk" ftype="genbank" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
202 <param name="fastq_input_selector" value="paired" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
203 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
204 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
205 <param name="minfrac" value="0.7" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
206 <param name="outputs" value="outgff,outsum" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
207 <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
208 <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
209 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
210
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
211 <test> <!-- test 6 - fasta ref default paired_collection -->
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
212 <param name="ref" value="wildtype.fna" ftype="fasta" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
213 <param name="fastq_input_selector" value="paired_collection" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
214 <param name="fastq_input">
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
215 <collection type="paired">
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
216 <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
217 <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
218 </collection>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
219 </param>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
220 <param name="outputs" value="outgff,outsum" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
221 <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
222 <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
223 </test>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
224
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
225 </tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
226
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
227
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
228 <help><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
229
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
230 **Snippy @VERSION@**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
231
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
232 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
233
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
234 **Author**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
235
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
236 Torsten Seemann
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
237
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
238 **Inputs**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
239
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
240 - NGS Reads in fastq format (single or paired end)
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
241 - Reference file in either fasta or genbank format
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
242
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
243 If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
244
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
245 **Advanced options**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
246
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
247 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
248
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
249 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
250
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
251 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
252
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
253 - rgid - String - Use this @RG ID: in the BAM header (default '')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
254
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
255 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
256
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
257 **Further information**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
258
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
259 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
260
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
261 ]]></help>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
262 <expand macro="citations"/>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
263
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
264 </tool>