Mercurial > repos > simon-gladman > snippy

comparison snippy.xml @ 9:234020dc16f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated to new version of snippy with static binaries
author simon-gladman
date Wed, 08 Jun 2016 02:56:35 -0400
parents 3b23249fe471
children 0c9f91faff96
comparison
equal deleted inserted replaced
8:3b23249fe471 9:234020dc16f7
1 <tool id="snippy" name="snippy" version="0.2.0"> 1 <tool id="snippy" name="snippy" version="0.3">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.0">snippy</requirement> 3 <requirement type="package" version="3.0">snippy</requirement>
4 <requirement type="package" version="1.2">samtools</requirement>
5 <requirement type="package" version="0.9.20">freebayes</requirement>
6 </requirements> 4 </requirements>
7 <stdio> 5 <stdio>
8 <exit_code range="1:" /> 6 <exit_code range="1:" />
9 </stdio> 7 </stdio>
10 8
11 <command><![CDATA[ 9 <command><![CDATA[
12 cp $ref foo.fna && 10 #if str( $reftype.ref_type_selector ) == "fasta"
11 cp $reftype.ref foo.fna &&
12 #end if
13 #if str( $reftype.ref_type_selector ) == "genbank"
14 cp $reftype.ref foo.gbk &&
15 #end if
13 snippy 16 snippy
14 --outdir out 17 --outdir out
15 --cpus "\${GALAXY_SLOTS:-1}" 18 --cpus "\${GALAXY_SLOTS:-1}"
16 --ref foo.fna 19 #if str( $reftype.ref_type_selector ) == "fasta"
20 --ref foo.fna
21 #end if
22 #if str( $reftype.ref_type_selector ) == "genbank"
23 --ref foo.gbk
24 #end if
17 $cleanup 25 $cleanup
18 #if str( $advanced.is_advanced ) == "advanced" 26 #if str( $advanced.is_advanced ) == "advanced"
19 --mapqual $advanced.mapqual 27 --mapqual $advanced.mapqual
20 --mincov $advanced.mincov 28 --mincov $advanced.mincov
21 --minfrac $advanced.minfrac 29 --minfrac $advanced.minfrac
46 gunzip out/snps.depth.gz 54 gunzip out/snps.depth.gz
47 55
48 56
49 ]]></command> 57 ]]></command>
50 <inputs> 58 <inputs>
51 <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" /> 59 <conditional name="reftype">
60 <param name="ref_type_selector" type="select" label="Reference type" help="File type of the reference file. (Fasta or Genbank)">
61 <option value="genbank">Genbank</option>
62 <option value="fasta">Fasta</option>
63 </param>
64 <when value="fasta">
65 <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" />
66 </when>
67 <when value="genbank">
68 <param name="ref" type="data" format="genbank" label="Reference Genbank" help="Genbank file to use as the reference" />
69 </when>
70 </conditional>
52 <conditional name="fastq_input"> 71 <conditional name="fastq_input">
53 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> 72 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
54 <option value="paired">Paired</option> 73 <option value="paired">Paired</option>
55 <option value="single">Single</option> 74 <option value="single">Single</option>
56 <option value="paired_collection">Paired Collection</option> 75 <option value="paired_collection">Paired Collection</option>
91 <outputs> 110 <outputs>
92 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/> 111 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/>
93 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/> 112 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>
94 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/> 113 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>
95 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/> 114 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>
96 <data format="text" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/> 115 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
97 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/> 116 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>
98 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/> 117 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
99 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/> 118 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
100 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> 119 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
101 <filter>cleanup is False</filter> 120 <filter>cleanup is False</filter>
102 </data> 121 </data>
103 </outputs> 122 </outputs>
104 123
105 <tests> 124 <tests>
106 <test> 125 <test>
126 <param name="ref_type_selector" value="fasta" />
107 <param name="ref" value="Ecoli.fna" ftype="fasta" /> 127 <param name="ref" value="Ecoli.fna" ftype="fasta" />
108 <param name="fastq_input_selector" value="paired" /> 128 <param name="fastq_input_selector" value="paired" />
109 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" /> 129 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" />
110 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" /> 130 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" />
111 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" /> 131 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" />
112 </test> 132 </test>
113 </tests> 133 </tests>
114 134
115 135
116 <help><![CDATA[ 136 <help><![CDATA[
117 This is a change to force a reinstall 137 Synopsis:
118 Synopsis:
119 snippy 3.0 - fast bacterial variant calling from NGS reads 138 snippy 3.0 - fast bacterial variant calling from NGS reads
139
120 Author: 140 Author:
121 Torsten Seemann <torsten.seemann@gmail.com> 141 Torsten Seemann <torsten.seemann@gmail.com>
142
122 Usage: 143 Usage:
123 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz> 144 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>
145
124 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq> 146 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>
147
125 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz> 148 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>
149
126 Options: 150 Options:
127 --help This help 151 --help This help
152
128 --version Print version and exit 153 --version Print version and exit
154
129 --citation Print citation for referencing snippy 155 --citation Print citation for referencing snippy
156
130 --quiet No screen output (default OFF) 157 --quiet No screen output (default OFF)
158
131 --cpus [N] Maximum number of CPU cores to use (default '8') 159 --cpus [N] Maximum number of CPU cores to use (default '8')
160
132 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '') 161 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
162
133 --outdir [X] Output folder (default '') 163 --outdir [X] Output folder (default '')
164
134 --prefix [X] Prefix for output files (default 'snps') 165 --prefix [X] Prefix for output files (default 'snps')
166
135 --force Force overwrite of existing output folder (default OFF) 167 --force Force overwrite of existing output folder (default OFF)
168
136 --pe1|R1|left [X] Reads, paired-end R1 (left) (default '') 169 --pe1|R1|left [X] Reads, paired-end R1 (left) (default '')
170
137 --pe2|R2|right [X] Reads, paired-end R2 (right) (default '') 171 --pe2|R2|right [X] Reads, paired-end R2 (right) (default '')
172
138 --se|single [X] Single-end reads (default '') 173 --se|single [X] Single-end reads (default '')
174
139 --peil [X] Reads, paired-end R1/R2 interleaved (default '') 175 --peil [X] Reads, paired-end R1/R2 interleaved (default '')
176
140 --mapqual [n.n] Minimum mapping quality to allow (default '60') 177 --mapqual [n.n] Minimum mapping quality to allow (default '60')
178
141 --mincov [N] Minimum coverage of variant site (default '10') 179 --mincov [N] Minimum coverage of variant site (default '10')
180
142 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9') 181 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9')
182
143 --report Produce long report with visual alignment (slow) (default OFF) 183 --report Produce long report with visual alignment (slow) (default OFF)
184
144 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF) 185 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF)
186
145 --rgid [X] Use this @RG ID: in the BAM header (default '') 187 --rgid [X] Use this @RG ID: in the BAM header (default '')
188
146 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '') 189 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')
147 190
148 ]]></help> 191 ]]></help>
149 192
150 <citations> 193 <citations>