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comparison cpo_snippy.xml @ 1:fea89c4d5227 draft

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author jjjjia
date Thu, 16 Aug 2018 19:27:05 -0400
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0:917a05a03ac9 1:fea89c4d5227
1 <tool id="snippy" name="snippy" version="3.2">
2 <requirements>
3 <requirement type="package" version="3.2">snippy</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8
9 <command>
10 <![CDATA[
11 snippy
12 --outdir out
13 --cpus "\${GALAXY_SLOTS:-1}"
14 --ref $ref
15 $cleanup
16 #if str( $advanced.is_advanced ) == "advanced"
17 --mapqual $advanced.mapqual
18 --mincov $advanced.mincov
19 --minfrac $advanced.minfrac
20 #if $advanced.rgid
21 --rgid $advanced.rgid
22 #end if
23 #if $advanced.bwaopt
24 --bwaopt $advanced.bwaopt
25 #end if
26 #end if
27 --ctgs $input
28
29 &&
30
31 gunzip out/snps.depth.gz
32
33 &&
34
35 tar -czf out.tgz out
36
37
38 ]]>
39 </command>
40 <inputs>
41
42 <param name="ref" type="data" format="fasta" label="Reference Fasta" />
43 <param name="input" type="data" format="fasta" label="assembled contigs"/>
44 <param name="cleanup" type="boolean" checked="true" truevalue="--cleanup" falsevalue="" label="Cleanup the non-snp output files" help="Remove all non-SNP files: BAMs, indices etc" />
45 <conditional name="advanced">
46 <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings">
47 <option value="advanced">Show advanced settings</option>
48 <option value="simple" selected="true">Hide advanced settings</option>
49 </param>
50 <when value="advanced">
51 <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
52 <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
53 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
54 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
55 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
56 </when>
57 <when value="simple">
58
59 </when>
60 </conditional>
61 </inputs>
62 <outputs>
63 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/>
64 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>
65 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>
66 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>
67 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
68 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>
69 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
70 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
71 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
72 <filter>cleanup is False</filter>
73 </data>
74 <data format="zip" name="outdir" label="${tool.name} on ${on_string} out dir" from_work_dir="out.tgz" />
75 </outputs>
76
77 <tests>
78 <test>
79 <param name="ref_type_selector" value="fasta" />
80 <param name="ref" value="Ecoli.fna" ftype="fasta" />
81 <param name="fastq_input_selector" value="paired" />
82 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" />
83 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" />
84 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" />
85 </test>
86 </tests>
87
88
89 <help>
90 <![CDATA[
91 Synopsis:
92 snippy 3.0 - fast bacterial variant calling from NGS reads
93
94 Author:
95 Torsten Seemann <torsten.seemann@gmail.com>
96
97 Usage:
98 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>
99
100 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>
101
102 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>
103
104 Options:
105 --help This help
106
107 --version Print version and exit
108
109 --citation Print citation for referencing snippy
110
111 --quiet No screen output (default OFF)
112
113 --cpus [N] Maximum number of CPU cores to use (default '8')
114
115 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
116
117 --outdir [X] Output folder (default '')
118
119 --prefix [X] Prefix for output files (default 'snps')
120
121 --force Force overwrite of existing output folder (default OFF)
122
123 --pe1|R1|left [X] Reads, paired-end R1 (left) (default '')
124
125 --pe2|R2|right [X] Reads, paired-end R2 (right) (default '')
126
127 --se|single [X] Single-end reads (default '')
128
129 --peil [X] Reads, paired-end R1/R2 interleaved (default '')
130
131 --mapqual [n.n] Minimum mapping quality to allow (default '60')
132
133 --mincov [N] Minimum coverage of variant site (default '10')
134
135 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9')
136
137 --report Produce long report with visual alignment (slow) (default OFF)
138
139 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF)
140
141 --rgid [X] Use this @RG ID: in the BAM header (default '')
142
143 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')
144
145 ]]>
146 </help>
147 <citations>
148 <citation type="bibtex">
149 @UNPUBLISHED{Seemann2013,
150 author = "Seemann T",
151 title = "snippy: fast bacterial variant calling from NGS reads",
152 year = "2015",
153 note = "https://github.com/tseemann/snippy"}
154 </citation>
155 </citations>
156
157
158 </tool>