snippy: snippy.xml annotate

annotate snippy.xml @ 9:234020dc16f7 draft

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

rev	line source
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	1 <tool id="snippy" name="snippy" version="0.3">
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	2 <requirements>
6 6ae77254acf4 Update to package_snippy_3_0 simon-gladman parents: 5 diff changeset	3 <requirement type="package" version="3.0">snippy</requirement>
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	4 </requirements>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	5 <stdio>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	6 <exit_code range="1:" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	7 </stdio>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	8
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	9 <command><![CDATA[
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	10 #if str( $reftype.ref_type_selector ) == "fasta"
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	11 cp $reftype.ref foo.fna &&
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	12 #end if
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	13 #if str( $reftype.ref_type_selector ) == "genbank"
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	14 cp $reftype.ref foo.gbk &&
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	15 #end if
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	16 snippy
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	17 --outdir out
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	18 --cpus "\${GALAXY_SLOTS:-1}"
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	19 #if str( $reftype.ref_type_selector ) == "fasta"
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	20 --ref foo.fna
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	21 #end if
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	22 #if str( $reftype.ref_type_selector ) == "genbank"
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	23 --ref foo.gbk
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	24 #end if
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	25 $cleanup
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	26 #if str( $advanced.is_advanced ) == "advanced"
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	27 --mapqual $advanced.mapqual
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	28 --mincov $advanced.mincov
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	29 --minfrac $advanced.minfrac
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	30 #if $advanced.rgid
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	31 --rgid $advanced.rgid
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	32 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	33 #if $advanced.bwaopt
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	34 --bwaopt $advanced.bwaopt
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	35 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	36 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	37 #if str( $fastq_input.fastq_input_selector ) == "paired"
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	38 --pe1 $fastq_input.fastq_input1
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	39 --pe2 $fastq_input.fastq_input2
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	40 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	41 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	42 --pe1 $fastq_input.fastq_input1.forward
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	43 --pe2 $fastq_input.fastq_input1.reverse
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	44 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	45 #if str( $fastq_input.fastq_input_selector ) == "single"
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	46 --se $fastq_input.fastq_input1
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	47 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	48 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	49 --peil $fastq_input.fastq_input1
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	50 #end if
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	51
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	52 &&
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	53
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	54 gunzip out/snps.depth.gz
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	55
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	56
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	57 ]]></command>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	58 <inputs>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	59 <conditional name="reftype">
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	60 <param name="ref_type_selector" type="select" label="Reference type" help="File type of the reference file. (Fasta or Genbank)">
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	61 <option value="genbank">Genbank</option>
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	62 <option value="fasta">Fasta</option>
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	63 </param>
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	64 <when value="fasta">
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	65 <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" />
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	66 </when>
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	67 <when value="genbank">
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	68 <param name="ref" type="data" format="genbank" label="Reference Genbank" help="Genbank file to use as the reference" />
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	69 </when>
234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	70 </conditional>
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	71 <conditional name="fastq_input">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	72 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	73 <option value="paired">Paired</option>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	74 <option value="single">Single</option>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	75 <option value="paired_collection">Paired Collection</option>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	76 <option value="paired_iv">Paired Interleaved</option>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	77 </param>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	78 <when value="paired">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	79 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	80 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	81 </when>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	82 <when value="single">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	83 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	84 </when>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	85 <when value="paired_collection">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	86 <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"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	87 </when>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	88 <when value="paired_iv">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	89 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	90 </when>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	91 </conditional>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	92 <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" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	93 <conditional name="advanced">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	94 <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	95 <option value="advanced">Show advanced settings</option>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	96 <option value="simple" selected="true">Hide advanced settings</option>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	97 </param>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	98 <when value="advanced">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	99 <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	100 <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	101 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	102 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	103 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	104 </when>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	105 <when value="simple">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	106
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	107 </when>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	108 </conditional>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	109 </inputs>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	110 <outputs>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	111 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	112 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	113 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	114 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	115 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	116 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	117 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	118 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	119 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	120 <filter>cleanup is False</filter>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	121 </data>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	122 </outputs>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	123
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	124 <tests>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	125 <test>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	126 <param name="ref_type_selector" value="fasta" />
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	127 <param name="ref" value="Ecoli.fna" ftype="fasta" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	128 <param name="fastq_input_selector" value="paired" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	129 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	130 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	131 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" />
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	132 </test>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	133 </tests>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	134
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	135
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	136 <help><![CDATA[
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	137 Synopsis:
7 1034b854d0ba Update to package_snippy_3_0 simon-gladman parents: 6 diff changeset	138 snippy 3.0 - fast bacterial variant calling from NGS reads
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	139
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	140 Author:
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	141 Torsten Seemann <torsten.seemann@gmail.com>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	142
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	143 Usage:
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	144 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	145
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	146 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	147
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	148 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	149
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	150 Options:
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	151 --help This help
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	152
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	153 --version Print version and exit
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	154
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	155 --citation Print citation for referencing snippy
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	156
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	157 --quiet No screen output (default OFF)
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	158
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	159 --cpus [N] Maximum number of CPU cores to use (default '8')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	160
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	161 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	162
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	163 --outdir [X] Output folder (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	164
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	165 --prefix [X] Prefix for output files (default 'snps')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	166
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	167 --force Force overwrite of existing output folder (default OFF)
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	168
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	169 --pe1\|R1\|left [X] Reads, paired-end R1 (left) (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	170
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	171 --pe2\|R2\|right [X] Reads, paired-end R2 (right) (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	172
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	173 --se\|single [X] Single-end reads (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	174
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	175 --peil [X] Reads, paired-end R1/R2 interleaved (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	176
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	177 --mapqual [n.n] Minimum mapping quality to allow (default '60')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	178
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	179 --mincov [N] Minimum coverage of variant site (default '10')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	180
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	181 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	182
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	183 --report Produce long report with visual alignment (slow) (default OFF)
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	184
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	185 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF)
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	186
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	187 --rgid [X] Use this @RG ID: in the BAM header (default '')
9 234020dc16f7 Updated to new version of snippy with static binaries simon-gladman parents: 8 diff changeset	188
0 da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	189 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	190
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	191 ]]></help>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	192
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	193 <citations>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	194 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	195 author = "Seemann T",
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	196 title = "snippy: fast bacterial variant calling from NGS reads",
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	197 year = "2015",
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	198 note = "https://github.com/tseemann/snippy"}
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	199 </citation>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	200 </citations>
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	201
da9e55d788b8 planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty simon-gladman parents: diff changeset	202 </tool>

Mercurial > repos > simon-gladman > snippy

annotate snippy.xml @ 9:234020dc16f7 draft