Mercurial > repos > iuc > snippy

annotate snippy.xml @ 13:d220115f882b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 4a4272101587c70abd11779660e77bc8718688e2"
author iuc
date Sat, 10 Jul 2021 07:46:31 +0000
parents fa016f1eea1a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
1 <tool id="snippy" name="snippy" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@">
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.
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
4 </description>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
5 <macros>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
6 <import>macros.xml</import>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
7 </macros>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
8 <expand macro="requirements" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
9 <expand macro="version_command" />
0
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
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
13 @REFERENCE_SOURCE_FILE@
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
14
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
15 #import re
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
16 #if str( $fastq_input.fastq_input_selector ) == "paired"
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
17 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
20 #elif str( $fastq_input.fastq_input_selector ) == "single"
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
22 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
23 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
24 #end if
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
25
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
26 snippy
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
27 --outdir '${dir_name}'
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
28 --cpus \${GALAXY_SLOTS:-1}
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
29 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
30 @REFERENCE_COMMAND@
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
31 --mapqual $adv.mapqual
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
32 --mincov $adv.mincov
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
33 --minfrac $adv.minfrac
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
34 --minqual $adv.minqual
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
35 #if $adv.rgid
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
36 --rgid '$adv.rgid'
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
37 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
38 #if $adv.bwaopt
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
39 --bwaopt '$adv.bwaopt'
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
40 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
41
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
42 #if str( $fastq_input.fastq_input_selector ) == "paired"
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
43 --R1 '$fastq_input.fastq_input1'
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
44 --R2 '$fastq_input.fastq_input2'
3
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
45 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
46 --R1 '$fastq_input.fastq_input.forward'
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
47 --R2 '$fastq_input.fastq_input.reverse'
3
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
48 #elif str( $fastq_input.fastq_input_selector ) == "single"
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
49 --se '$fastq_input.fastq_input_single'
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
50 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
51 --peil '$fastq_input.fastq_input_interleaved'
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
52 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
53
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
54 #if "outcon" in str($outputs) and $adv.rename_cons
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
55 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
56 #end if
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
57
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
58 && cp -r '${dir_name}' out
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
59 && tar -czf out.tgz '${dir_name}'
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
60 ]]> </command>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
61
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
62 <inputs>
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
63 <expand macro="reference_selector" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
64 <conditional name="fastq_input">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65 <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
66 <option value="paired">Paired</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67 <option value="single">Single</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
68 <option value="paired_collection">Paired Collection</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
69 <option value="paired_iv">Paired Interleaved</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
70 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71 <when value="paired">
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
72 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
73 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
74 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
75 <when value="single">
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
76 <param name="fastq_input_single" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
77 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
78 <when value="paired_collection">
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
79 <param name="fastq_input" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" 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
80 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
81 <when value="paired_iv">
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
82 <param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
83 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
84 </conditional>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
85
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
86 <section name="adv" title="Advanced parameters" expanded="false">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
87 <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
88 <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
89 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
90 <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
91 <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
92 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
93 <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
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
94 </section>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
95
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
96 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
97 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
98 <option value="outgff" selected="False">The variants in GFF3 format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
99 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
100 <option value="outsum" selected="False">A summary of the samples and mapping</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
101 <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
102 <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
103 <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
104 <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
105 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
106 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
107
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
108 </inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
109
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
110 <outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
111
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
112 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
113 <filter>outputs and 'outvcf' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
114 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
115 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
116 <filter>outputs and 'outgff' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
117 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
118 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
119 <filter>outputs and 'outtab' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
120 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
121 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
122 <filter>outputs and 'outsum' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
123 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
124 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
125 <filter>outputs and 'outlog' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
126 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
127 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
128 <filter>outputs and 'outaln' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
129 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
130 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
131 <filter>outputs and 'outcon' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
132 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
133 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
134 <filter>outputs and 'outbam' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
135 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
136 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
137 <filter>outputs and 'outzip' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
138 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
139
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
140 </outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
141
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
142 <tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
143
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
144 <test> <!-- test 0 - fasta ref no snps -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
145 <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
146 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
147 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
148 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
149 </conditional>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
150 <param name="fastq_input_selector" value="paired" />
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
151 <param name="fastq_input1" ftype="fastqsanger.gz" value="a_1.fastq.gz" />
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
152 <param name="fastq_input2" ftype="fastqsanger.gz" value="a_2.fastq.gz" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
153 <param name="mincov" value="2" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
154 <param name="minqual" value="60" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
155 <param name="outputs" value="outgff,outsum" />
11
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
156 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
157 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
158 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
159
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
160 <test> <!-- test 1 - fasta ref one snp -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
161 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
162 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
163 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
164 </conditional>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
165 <param name="fastq_input_selector" value="paired" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
166 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
167 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
168 <param name="mincov" value="2" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
169 <param name="minqual" value="60" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
170 <param name="outputs" value="outgff,outsum" />
11
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
171 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
172 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
173 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
174
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
175 <test> <!-- test 2 - fasta ref one snp paired_collection -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
176 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
177 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
178 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
179 </conditional>
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
180 <param name="fastq_input_selector" value="paired_collection" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
181 <param name="fastq_input">
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
182 <collection type="paired">
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
183 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
184 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
185 </collection>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
186 </param>
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
187 <param name="mincov" value="2" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
188 <param name="minqual" value="60" />
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
189 <param name="outputs" value="outgff,outsum" />
11
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
190 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
191 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
1
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
192 </test>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61
iuc
parents: 0
diff changeset
193
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
194 <test> <!-- test 3 - fasta ref one snp single -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
195 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
196 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
197 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
198 </conditional>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
199 <param name="fastq_input_selector" value="single" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
200 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
201 <param name="mincov" value="2" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
202 <param name="minqual" value="60" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
203 <param name="outputs" value="outgff,outsum" />
11
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
204 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
205 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
206 </test>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
207
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
208 <test> <!-- test 4 - reference source as cached -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
209 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
210 <param name="reference_source_selector" value="cached"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
211 <param name="ref_file" value="test_id"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
212 </conditional>
3
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
213 <param name="fastq_input_selector" value="single" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
214 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
215 <param name="mincov" value="2" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
216 <param name="minqual" value="60" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
217 <param name="outputs" value="outgff,outsum" />
11
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
218 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
5bbf9eada9c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit e3844d13b58d22b269b986e03177e6f5efb675b4"
iuc
parents: 9
diff changeset
219 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
3
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
iuc
parents: 2
diff changeset
220 </test>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
221 </tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
222
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
223
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
224 <help><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
225
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
226 **Snippy @VERSION@**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
227
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
228 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
229
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
230 **Author**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
231
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
232 Torsten Seemann
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
233
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
234 **Inputs**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
235
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
236 - NGS Reads in fastq format (single or paired end)
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
237 - Reference file in either fasta or genbank format
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
238
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
239 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
240
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
241 **Advanced options**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
242
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
243 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
244
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
245 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
246
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
247 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
248
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
249 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 1
diff changeset
250
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
251 - rgid - String - Use this @RG ID: in the BAM header (default '')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
252
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
253 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
254
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
255 **Further information**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
256
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
257 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
258
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
259 ]]> </help>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 3
diff changeset
260 <expand macro="citations"/>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
261
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
262 </tool>