snippy: snippy.xml annotate

annotate snippy.xml @ 1:d4e6df2bc5e8 draft

planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61

author	iuc
date	Sat, 26 Jan 2019 14:36:18 -0500
parents	ff177a01b5ca
children	4eb9595bff60

rev	line source
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	2 <description>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	4 </description>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	5 <macros>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	6 <import>macros.xml</import>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	7 </macros>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	8 <expand macro="requirements" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	9 <expand macro="version_command" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	10
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	12
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	13 #if $ref.is_of_type("fasta")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	14 cp '$ref' 'foo.fna' &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	15 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	16 #if $ref.is_of_type("genbank")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	17 cp '$ref' 'foo.gbk' &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	18 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	19 snippy
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	20 --outdir 'out'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	21 --cpus "\${GALAXY_SLOTS:-1}"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	22 #if $ref.is_of_type("fasta")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	23 --ref 'foo.fna'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	24 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	25 #if $ref.is_of_type("genbank")
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	26 --ref 'foo.gbk'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	27 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	28 --mapqual $adv.mapqual
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	29 --mincov $adv.mincov
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	30 --minfrac $adv.minfrac
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	31 #if $adv.rgid
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	32 --rgid '$advanced.rgid'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	33 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	34 #if $adv.bwaopt
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	35 --bwaopt '$advanced.bwaopt'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	36 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	37
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	38 #if str( $fastq_input.fastq_input_selector ) == "paired"
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	39 --pe1 '$fastq_input.fastq_input1'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	40 --pe2 '$fastq_input.fastq_input2'
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	41 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	42 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	43 --pe1 '$fastq_input.fastq_input.forward'
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	44 --pe2 '$fastq_input.fastq_input.reverse'
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	45 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	46 #if str( $fastq_input.fastq_input_selector ) == "single"
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	47 --se '$fastq_input.fastq_input'
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	48 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	49 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	50 --peil '$fastq_input.fastq_input'
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	51 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	52
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	53 &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	54
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	55 gunzip out/snps.depth.gz
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	56
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	57 &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	58
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	59 #import re
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	60 #if str( $fastq_input.fastq_input_selector ) == "paired"
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	61 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	62 #else
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	63 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	64 #end if
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	65
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	66 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	67 tar -czf out.tgz ${dir_name}
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	68
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	69
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	70 ]]></command>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	71
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	72 <inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	73
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	74 <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	75
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	76 <conditional name="fastq_input">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	77 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	78 <option value="paired">Paired</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	79 <option value="single">Single</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	80 <option value="paired_collection">Paired Collection</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	81 <option value="paired_iv">Paired Interleaved</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	82 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	83 <when value="paired">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	84 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	85 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	86 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	87 <when value="single">
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	88 <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	89 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	90 <when value="paired_collection">
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	91 <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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	92 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	93 <when value="paired_iv">
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	94 <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	95 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	96 </conditional>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	97
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	98 <section name="adv" title="Advanced parameters" expanded="false">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	99 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	100 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	101 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	102 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	103 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	104 </section>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	105
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	106 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	107 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	108 <option value="outgff" selected="False">The variants in GFF3 format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	109 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	110 <option value="outsum" selected="False">A summary of the samples and mapping</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	111 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	112 <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>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	113 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	114 <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	115 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	116 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	117 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	118
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	119 </inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	120
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	121 <outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	122
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	123 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	124 <filter>outputs and 'outvcf' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	125 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	126 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	127 <filter>outputs and 'outgff' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	128 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	129 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	130 <filter>outputs and 'outtab' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	131 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	132 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	133 <filter>outputs and 'outsum' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	134 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	135 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	136 <filter>outputs and 'outlog' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	137 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	138 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	139 <filter>outputs and 'outaln' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	140 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	141 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	142 <filter>outputs and 'outcon' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	143 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	144 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	145 <filter>outputs and 'outdep' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	146 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	147 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	148 <filter>outputs and 'outbam' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	149 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	150 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	151 <filter>outputs and 'outzip' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	152 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	153
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	154 </outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	155
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	156 <tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	157
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	158 <test> <!-- test 1 - fasta ref default -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	159 <param name="ref" value="wildtype.fna" ftype="fasta" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	160 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	161 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	162 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	163 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	164 <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	165 <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	166 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	167
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	168 <test> <!-- test 2 - gbk ref default -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	169 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	170 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	171 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	172 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	173 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	174 <output name="snpsum" ftype="tabular" file="gbk_ref/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	175 <output name="snpgff" ftype="gff3" file="gbk_ref/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	176 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	177
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	178 <test> <!-- test 3 - gbk mapqual=40 -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	179 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	180 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	181 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	182 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	183 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	184 <param name="mapqual" value="40" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	185 <output name="snpsum" ftype="tabular" file="map_qual/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	186 <output name="snpgff" ftype="gff3" file="map_qual/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	187 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	188
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	189 <test> <!-- test 4 - gbk mincov=15 -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	190 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	191 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	192 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	193 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	194 <param name="mincov" value="15" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	195 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	196 <output name="snpsum" ftype="tabular" file="min_cov/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	197 <output name="snpgff" ftype="gff3" file="min_cov/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	198 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	199
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	200 <test> <!-- test 5 - gbk minfrac=0.7 -->
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	201 <param name="ref" value="wildtype.gbk" ftype="genbank" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	202 <param name="fastq_input_selector" value="paired" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	203 <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	204 <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	205 <param name="minfrac" value="0.7" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	206 <param name="outputs" value="outgff,outsum" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	207 <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	208 <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	209 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	210
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	211 <test> <!-- test 6 - fasta ref default paired_collection -->
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	212 <param name="ref" value="wildtype.fna" ftype="fasta" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	213 <param name="fastq_input_selector" value="paired_collection" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	214 <param name="fastq_input">
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	215 <collection type="paired">
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	216 <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	217 <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	218 </collection>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	219 </param>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	220 <param name="outputs" value="outgff,outsum" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	221 <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	222 <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	223 </test>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	224
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	225 </tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	226
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	227
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	228 <help><![CDATA[
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	229
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	230 Snippy @VERSION@
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	231
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	232 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	233
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	234 Author
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	235
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	236 Torsten Seemann
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	237
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	238 Inputs
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	239
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	240 - NGS Reads in fastq format (single or paired end)
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	241 - Reference file in either fasta or genbank format
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	242
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	243 If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	244
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	245 Advanced options
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	246
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	247 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	248
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	249 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	250
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	251 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	252
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	253 - rgid - String - Use this @RG ID: in the BAM header (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	254
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	255 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	256
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	257 Further information
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	258
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	259 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	260
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	261 ]]></help>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	262 <expand macro="citations"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	263
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	264 </tool>

Mercurial > repos > iuc > snippy

annotate snippy.xml @ 1:d4e6df2bc5e8 draft