Mercurial > repos > simon-gladman > snippy
comparison snippy.xml @ 0:0801bffdfcc8 draft
Initial upload
author | simon-gladman |
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date | Sun, 05 Jun 2016 21:12:39 -0400 |
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children | e1b47f2236b6 |
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1 <tool id="snippy" name="snippy" version="0.2.0"> | |
2 <requirements> | |
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> | |
7 <stdio> | |
8 <exit_code range="1:" /> | |
9 </stdio> | |
10 | |
11 <command><![CDATA[ | |
12 cp $ref foo.fna && | |
13 snippy | |
14 --outdir out | |
15 --cpus "\${GALAXY_SLOTS:-1}" | |
16 --ref foo.fna | |
17 $cleanup | |
18 #if str( $advanced.is_advanced ) == "advanced" | |
19 --mapqual $advanced.mapqual | |
20 --mincov $advanced.mincov | |
21 --minfrac $advanced.minfrac | |
22 #if $advanced.rgid | |
23 --rgid $advanced.rgid | |
24 #end if | |
25 #if $advanced.bwaopt | |
26 --bwaopt $advanced.bwaopt | |
27 #end if | |
28 #end if | |
29 #if str( $fastq_input.fastq_input_selector ) == "paired" | |
30 --pe1 $fastq_input.fastq_input1 | |
31 --pe2 $fastq_input.fastq_input2 | |
32 #end if | |
33 #if str( $fastq_input.fastq_input_selector ) == "paired_collection" | |
34 --pe1 $fastq_input.fastq_input1.forward | |
35 --pe2 $fastq_input.fastq_input1.reverse | |
36 #end if | |
37 #if str( $fastq_input.fastq_input_selector ) == "single" | |
38 --se $fastq_input.fastq_input1 | |
39 #end if | |
40 #if str( $fastq_input.fastq_input_selector ) == "paired_iv" | |
41 --peil $fastq_input.fastq_input1 | |
42 #end if | |
43 | |
44 && | |
45 | |
46 gunzip out/snps.depth.gz | |
47 | |
48 | |
49 ]]></command> | |
50 <inputs> | |
51 <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" /> | |
52 <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"> | |
54 <option value="paired">Paired</option> | |
55 <option value="single">Single</option> | |
56 <option value="paired_collection">Paired Collection</option> | |
57 <option value="paired_iv">Paired Interleaved</option> | |
58 </param> | |
59 <when value="paired"> | |
60 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> | |
61 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> | |
62 </when> | |
63 <when value="single"> | |
64 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> | |
65 </when> | |
66 <when value="paired_collection"> | |
67 <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> | |
68 </when> | |
69 <when value="paired_iv"> | |
70 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> | |
71 </when> | |
72 </conditional> | |
73 <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" /> | |
74 <conditional name="advanced"> | |
75 <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings"> | |
76 <option value="advanced">Show advanced settings</option> | |
77 <option value="simple" selected="true">Hide advanced settings</option> | |
78 </param> | |
79 <when value="advanced"> | |
80 <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> | |
81 <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" /> | |
82 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" /> | |
83 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" /> | |
84 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" /> | |
85 </when> | |
86 <when value="simple"> | |
87 | |
88 </when> | |
89 </conditional> | |
90 </inputs> | |
91 <outputs> | |
92 <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 ${on_string} snps gff file" from_work_dir="out/snps.gff"/> | |
94 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/> | |
95 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/> | |
96 <data format="text" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/> | |
97 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/> | |
98 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/> | |
99 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/> | |
100 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> | |
101 <filter>cleanup is False</filter> | |
102 </data> | |
103 </outputs> | |
104 | |
105 <tests> | |
106 <test> | |
107 <param name="ref" value="Ecoli.fna" ftype="fasta" /> | |
108 <param name="fastq_input_selector" value="paired" /> | |
109 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" /> | |
110 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" /> | |
111 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" /> | |
112 </test> | |
113 </tests> | |
114 | |
115 | |
116 <help><![CDATA[ | |
117 This is a change to force a reinstall | |
118 Synopsis: | |
119 snippy 3.0 - fast bacterial variant calling from NGS reads | |
120 Author: | |
121 Torsten Seemann <torsten.seemann@gmail.com> | |
122 Usage: | |
123 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz> | |
124 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq> | |
125 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz> | |
126 Options: | |
127 --help This help | |
128 --version Print version and exit | |
129 --citation Print citation for referencing snippy | |
130 --quiet No screen output (default OFF) | |
131 --cpus [N] Maximum number of CPU cores to use (default '8') | |
132 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '') | |
133 --outdir [X] Output folder (default '') | |
134 --prefix [X] Prefix for output files (default 'snps') | |
135 --force Force overwrite of existing output folder (default OFF) | |
136 --pe1|R1|left [X] Reads, paired-end R1 (left) (default '') | |
137 --pe2|R2|right [X] Reads, paired-end R2 (right) (default '') | |
138 --se|single [X] Single-end reads (default '') | |
139 --peil [X] Reads, paired-end R1/R2 interleaved (default '') | |
140 --mapqual [n.n] Minimum mapping quality to allow (default '60') | |
141 --mincov [N] Minimum coverage of variant site (default '10') | |
142 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9') | |
143 --report Produce long report with visual alignment (slow) (default OFF) | |
144 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF) | |
145 --rgid [X] Use this @RG ID: in the BAM header (default '') | |
146 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '') | |
147 | |
148 ]]></help> | |
149 | |
150 <citations> | |
151 <citation type="bibtex">@UNPUBLISHED{Seemann2013, | |
152 author = "Seemann T", | |
153 title = "snippy: fast bacterial variant calling from NGS reads", | |
154 year = "2015", | |
155 note = "https://github.com/tseemann/snippy"} | |
156 </citation> | |
157 </citations> | |
158 | |
159 </tool> |