Mercurial > repos > dfornika > snippy

annotate snippy.xml @ 32:3ac93a6e4687 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
author dfornika
date Sat, 25 Jan 2020 00:50:20 +0000
parents 20b52007c4dc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
2 <description>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
4 </description>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
5 <macros>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
6 <import>macros.xml</import>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
7 </macros>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
8 <expand macro="requirements" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
9 <expand macro="version_command" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
10
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
12
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
13 @REFERENCE_SOURCE_FILE@
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
14
25
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
15 #import re
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
16 #if str( $fastq_input.fastq_input_selector ) == "paired"
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
17 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
20 #elif str( $fastq_input.fastq_input_selector ) == "single"
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
22 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
23 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
24 #end if
ae9dffe91f20 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 24
diff changeset
25
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
26 snippy
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
27 --outdir '${dir_name}'
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
28 --cpus \${GALAXY_SLOTS:-1}
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
29 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
30 @REFERENCE_COMMAND@
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
31 --mapqual $adv.mapqual
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
32 --mincov $adv.mincov
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
33 --minfrac $adv.minfrac
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
34 --minqual $adv.minqual
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
35 #if $adv.rgid
21
0e733df972b5 planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents: 20
diff changeset
36 --rgid '$adv.rgid'
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
37 #end if
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
38 #if $adv.bwaopt
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
39 --bwaopt '$adv.bwaopt'
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
40 #end if
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
41
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
42 #if str( $fastq_input.fastq_input_selector ) == "paired"
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
43 --R1 '$fastq_input.fastq_input1'
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
44 --R2 '$fastq_input.fastq_input2'
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
45 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
46 --R1 '$fastq_input.fastq_input.forward'
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
47 --R2 '$fastq_input.fastq_input.reverse'
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
48 #elif str( $fastq_input.fastq_input_selector ) == "single"
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
49 --se '$fastq_input.fastq_input_single'
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
50 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
51 --peil '$fastq_input.fastq_input_interleaved'
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
52 #end if
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
53
21
0e733df972b5 planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents: 20
diff changeset
54 #if "outcon" in str($outputs) and $adv.rename_cons
32
3ac93a6e4687 "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 30
diff changeset
55 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
21
0e733df972b5 planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
dfornika
parents: 20
diff changeset
56 #end if
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
57
32
3ac93a6e4687 "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 30
diff changeset
58 && cp -r '${dir_name}' out
3ac93a6e4687 "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 30
diff changeset
59 && tar -czf out.tgz '${dir_name}'
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
60 ]]> </command>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
61
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
62 <inputs>
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
63 <expand macro="reference_selector" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
64 <conditional name="fastq_input">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
66 <option value="paired">Paired</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
67 <option value="single">Single</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
68 <option value="paired_collection">Paired Collection</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
69 <option value="paired_iv">Paired Interleaved</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
70 </param>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
71 <when value="paired">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
72 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
73 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
74 </when>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
75 <when value="single">
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
76 <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
77 </when>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
78 <when value="paired_collection">
14
b102aece6b65 planemo upload for repository https://github.com/tseemann/snippy commit 93b22331ca83a82fdfbe8f2b274577e21f9bf025-dirty
dfornika
parents: 6
diff changeset
79 <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
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
80 </when>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
81 <when value="paired_iv">
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
82 <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
83 </when>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
84 </conditional>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
85
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
86 <section name="adv" title="Advanced parameters" expanded="false">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
87 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
88 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
89 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
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
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
91 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
92 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
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
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
94 </section>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
95
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
96 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
97 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
98 <option value="outgff" selected="False">The variants in GFF3 format</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
99 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
100 <option value="outsum" selected="False">A summary of the samples and mapping</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
101 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
103 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
105 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
106 </param>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
107
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
108 </inputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
109
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
110 <outputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
111
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
112 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
113 <filter>outputs and 'outvcf' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
114 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
115 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
116 <filter>outputs and 'outgff' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
117 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
118 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
119 <filter>outputs and 'outtab' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
120 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
121 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
122 <filter>outputs and 'outsum' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
123 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
124 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
125 <filter>outputs and 'outlog' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
126 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
127 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
128 <filter>outputs and 'outaln' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
129 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
130 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
131 <filter>outputs and 'outcon' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
132 </data>
26
15d5dd95daf2 planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
dfornika
parents: 25
diff changeset
133 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
134 <filter>outputs and 'outbam' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
135 </data>
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
136 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
137 <filter>outputs and 'outzip' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
138 </data>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
139
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
140 </outputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
141
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
142 <tests>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
143
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
144 <test> <!-- test 0 - fasta ref no snps -->
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
145 <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
146 <conditional name="reference_source">
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
147 <param name="reference_source_selector" value="history"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
148 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
149 </conditional>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
150 <param name="fastq_input_selector" value="paired" />
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
151 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
152 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
153 <param name="mincov" value="2" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
154 <param name="minqual" value="60" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
155 <param name="outputs" value="outgff,outsum" />
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
156 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
157 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
158 </test>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
159
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
160 <test> <!-- test 1 - fasta ref one snp -->
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
161 <conditional name="reference_source">
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
162 <param name="reference_source_selector" value="history"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
163 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
164 </conditional>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
165 <param name="fastq_input_selector" value="paired" />
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
166 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
167 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
168 <param name="mincov" value="2" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
169 <param name="minqual" value="60" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
170 <param name="outputs" value="outgff,outsum" />
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
171 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
172 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
173 </test>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
174
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
175 <test> <!-- test 2 - fasta ref one snp paired_collection -->
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
176 <conditional name="reference_source">
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
177 <param name="reference_source_selector" value="history"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
178 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
179 </conditional>
19
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
180 <param name="fastq_input_selector" value="paired_collection" />
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
181 <param name="fastq_input">
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
182 <collection type="paired">
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
183 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
184 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
19
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
185 </collection>
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
186 </param>
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
187 <param name="mincov" value="2" />
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
188 <param name="minqual" value="60" />
19
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
189 <param name="outputs" value="outgff,outsum" />
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
190 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
191 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
19
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
192 </test>
8a6b951f6ec2 planemo upload for repository https://github.com/tseemann/snippy commit 80a4218b47696bea243b4092823739a578ea8652-dirty
dfornika
parents: 14
diff changeset
193
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
194 <test> <!-- test 3 - fasta ref one snp single -->
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
195 <conditional name="reference_source">
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
196 <param name="reference_source_selector" value="history"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
197 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
198 </conditional>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
199 <param name="fastq_input_selector" value="single" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
200 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
201 <param name="mincov" value="2" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
202 <param name="minqual" value="60" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
203 <param name="outputs" value="outgff,outsum" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
204 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
205 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
206 </test>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
207
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
208 <test> <!-- test 4 - reference source as cached -->
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
209 <conditional name="reference_source">
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
210 <param name="reference_source_selector" value="cached"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
211 <param name="ref_file" value="test_id"/>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
212 </conditional>
22
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
213 <param name="fastq_input_selector" value="single" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
214 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
215 <param name="mincov" value="2" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
216 <param name="minqual" value="60" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
217 <param name="outputs" value="outgff,outsum" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
218 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
219 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
0bf16c8aca73 planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
dfornika
parents: 21
diff changeset
220 </test>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
221 </tests>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
222
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
223
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
224 <help><![CDATA[
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
225
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
226 **Snippy @VERSION@**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
227
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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).
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
229
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
230 **Author**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
231
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
232 Torsten Seemann
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
233
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
234 **Inputs**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
235
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
236 - NGS Reads in fastq format (single or paired end)
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
237 - Reference file in either fasta or genbank format
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
238
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
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.
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
240
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
241 **Advanced options**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
242
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
243 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
244
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
245 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
246
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
247 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
248
20
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
249 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty
dfornika
parents: 19
diff changeset
250
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
251 - rgid - String - Use this @RG ID: in the BAM header (default '')
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
252
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
253 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
254
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
255 **Further information**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
256
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
257 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
258
29
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
259 ]]> </help>
62329bafeaef "planemo upload commit f1b3e36f79747fca391321389276ac196d3f7cd0-dirty"
dfornika
parents: 28
diff changeset
260 <expand macro="citations"/>
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
261
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
262 </tool>