Mercurial > repos > iuc > snippy

annotate snippy.xml @ 2:4eb9595bff60 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
author iuc
date Mon, 18 Mar 2019 10:58:41 -0400
parents d4e6df2bc5e8
children a2147b3769dd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
0
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 $ref.is_of_type("fasta")
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
14 cp '$ref' 'ref.fna' &&
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
15 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
16 #if $ref.is_of_type("genbank")
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
17 cp '$ref' 'ref.gbk' &&
0
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'
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
21 --cpus \${GALAXY_SLOTS:-1}
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
22 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
23 #if $ref.is_of_type("fasta")
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
24 --ref 'ref.fna'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
25 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
26 #if $ref.is_of_type("genbank")
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
27 --ref 'ref.gbk'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
28 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
29 --mapqual $adv.mapqual
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
30 --mincov $adv.mincov
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
31 --minfrac $adv.minfrac
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
32 --minqual $adv.minqual
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
33 #if $adv.rgid
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
34 --rgid '$adv.rgid'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
35 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
36 #if $adv.bwaopt
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
37 --bwaopt '$adv.bwaopt'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
38 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
39
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
40 #if str( $fastq_input.fastq_input_selector ) == "paired"
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
41 --R1 '$fastq_input.fastq_input1'
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
42 --R2 '$fastq_input.fastq_input2'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
43 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
44 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
45 --R1 '$fastq_input.fastq_input.forward'
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
46 --R2 '$fastq_input.fastq_input.reverse'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
47 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
48 #if str( $fastq_input.fastq_input_selector ) == "single"
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
49 --se '$fastq_input.fastq_input'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
50 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
51 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
52 --peil '$fastq_input.fastq_input'
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
53 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
54
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
55 &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
56
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
57 #import re
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
58 #if str( $fastq_input.fastq_input_selector ) == "paired"
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
59 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
60 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
61 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
62 #else
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
63 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
64 #end if
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
66 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67 tar -czf out.tgz ${dir_name}
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
68 #if "outcon" in str($outputs) and $adv.rename_cons
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
69 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
70 #end if
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
72
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
73 ]]></command>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
74
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
75 <inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
76
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
77 <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
78
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
79 <conditional name="fastq_input">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
80 <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
81 <option value="paired">Paired</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
82 <option value="single">Single</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
83 <option value="paired_collection">Paired Collection</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
84 <option value="paired_iv">Paired Interleaved</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
85 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
86 <when value="paired">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
87 <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
88 <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
89 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
90 <when value="single">
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
91 <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
92 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
93 <when value="paired_collection">
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
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"/>
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
95 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
96 <when value="paired_iv">
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
97 <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
98 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
99 </conditional>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
100
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
101 <section name="adv" title="Advanced parameters" expanded="false">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
102 <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
103 <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
104 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
105 <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
106 <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
107 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
108 <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
109 </section>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
110
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
111 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
112 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
113 <option value="outgff" selected="False">The variants in GFF3 format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
114 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
115 <option value="outsum" selected="False">A summary of the samples and mapping</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
116 <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
117 <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
118 <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
119 <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
120 <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
121 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
122 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
123
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
124 </inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
125
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
126 <outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
127
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
128 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
129 <filter>outputs and 'outvcf' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
130 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
131 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
132 <filter>outputs and 'outgff' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
133 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
134 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
135 <filter>outputs and 'outtab' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
136 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
137 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
138 <filter>outputs and 'outsum' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
139 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
140 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
141 <filter>outputs and 'outlog' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
142 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
143 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
144 <filter>outputs and 'outaln' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
145 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
146 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
147 <filter>outputs and 'outcon' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
148 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
149 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
150 <filter>outputs and 'outdep' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
151 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
152 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
153 <filter>outputs and 'outbam' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
154 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
155 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
156 <filter>outputs and 'outzip' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
157 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
158
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
159 </outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
160
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
161 <tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
162
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
163 <test> <!-- test 0 - fasta ref no snps -->
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
164 <param name="ref" value="reference.fasta" ftype="fasta" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
165 <param name="fastq_input_selector" value="paired" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
166 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
167 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
168 <param name="mincov" value="2" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
169 <param name="minqual" value="60" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
170 <param name="outputs" value="outgff,outsum" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
171 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
172 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
173 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
174
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
175 <test> <!-- test 1 - fasta ref one snp -->
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
176 <param name="ref" value="reference.fasta" ftype="fasta" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
177 <param name="fastq_input_selector" value="paired" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
178 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
179 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
180 <param name="mincov" value="2" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
181 <param name="minqual" value="60" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
182 <param name="outputs" value="outgff,outsum" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
183 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
184 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
185 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
186
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
187 <test> <!-- test 2 - fasta ref one snp paired_collection -->
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
188 <param name="ref" value="reference.fasta" ftype="fasta" />
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
189 <param name="fastq_input_selector" value="paired_collection" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
190 <param name="fastq_input">
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
191 <collection type="paired">
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
192 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
193 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
194 </collection>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
195 </param>
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
196 <param name="mincov" value="2" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
197 <param name="minqual" value="60" />
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
198 <param name="outputs" value="outgff,outsum" />
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
199 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
200 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
1
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
201 </test>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
202
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
203 </tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
204
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
205
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
206 <help><![CDATA[
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
207
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
208 **Snippy @VERSION@**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
209
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
210 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
211
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
212 **Author**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
213
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
214 Torsten Seemann
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
215
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
216 **Inputs**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
217
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
218 - NGS Reads in fastq format (single or paired end)
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
219 - Reference file in either fasta or genbank format
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
220
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
221 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
222
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
223 **Advanced options**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
224
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
225 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
226
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
227 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
228
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
229 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
230
2
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
231 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
232
0
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
233 - rgid - String - Use this @RG ID: in the BAM header (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
234
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
235 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
236
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
237 **Further information**
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
238
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
239 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
240
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
241 ]]></help>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
242 <expand macro="citations"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
243
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
244 </tool>