snippy: snippy.xml annotate

annotate snippy.xml @ 8:32f2211eeec3 draft

"planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7"

author	iuc
date	Sun, 01 Dec 2019 13:06:05 -0500
parents	e32aac2299fb
children	e4d0231d8595

rev	line source
8 32f2211eeec3 "planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7" iuc parents: 7 diff changeset	1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	2 <description>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	4 </description>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	5 <macros>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	6 <import>macros.xml</import>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	7 </macros>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	8 <expand macro="requirements" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	9 <expand macro="version_command" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	10
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	12
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	13 @REFERENCE_SOURCE_FILE@
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	14
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	15 snippy
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	16 --outdir 'out'
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	17 --cpus \${GALAXY_SLOTS:-1}
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	18 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	19 @REFERENCE_COMMAND@
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	20 --mapqual $adv.mapqual
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	21 --mincov $adv.mincov
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	22 --minfrac $adv.minfrac
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	23 --minqual $adv.minqual
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	24 #if $adv.rgid
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	25 --rgid '$adv.rgid'
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	26 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	27 #if $adv.bwaopt
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	28 --bwaopt '$adv.bwaopt'
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	29 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	30
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	31 #if str( $fastq_input.fastq_input_selector ) == "paired"
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	32 --R1 '$fastq_input.fastq_input1'
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	33 --R2 '$fastq_input.fastq_input2'
3 feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	34 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	35 --R1 '$fastq_input.fastq_input.forward'
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	36 --R2 '$fastq_input.fastq_input.reverse'
3 feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	37 #elif str( $fastq_input.fastq_input_selector ) == "single"
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	38 --se '$fastq_input.fastq_input_single'
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	39 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	40 --peil '$fastq_input.fastq_input_interleaved'
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	41 #end if
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	42
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	43 &&
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	44
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	45 #import re
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	46 #if str( $fastq_input.fastq_input_selector ) == "paired"
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	47 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	48 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	49 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
3 feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	50 #elif str( $fastq_input.fastq_input_selector ) == "single"
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	51 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	53 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	54 #end if
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	55
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	56 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
8 32f2211eeec3 "planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7" iuc parents: 7 diff changeset	57 tar -czf out.tgz ${dir_name}
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	58 #if "outcon" in str($outputs) and $adv.rename_cons
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	59 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	60 #end if
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	61
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	62
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	63 ]]> </command>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	64
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	65 <inputs>
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	66 <expand macro="reference_selector" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	67 <conditional name="fastq_input">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	68 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	69 <option value="paired">Paired</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	70 <option value="single">Single</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	71 <option value="paired_collection">Paired Collection</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	72 <option value="paired_iv">Paired Interleaved</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	73 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	74 <when value="paired">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	75 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	76 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	77 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	78 <when value="single">
3 feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	79 <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	80 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	81 <when value="paired_collection">
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	82 <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 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	83 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	84 <when value="paired_iv">
3 feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	85 <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	86 </when>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	87 </conditional>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	88
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	89 <section name="adv" title="Advanced parameters" expanded="false">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	90 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	91 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	92 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	93 <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	94 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	95 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	96 <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	97 </section>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	98
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	99 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	100 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	101 <option value="outgff" selected="False">The variants in GFF3 format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	102 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	103 <option value="outsum" selected="False">A summary of the samples and mapping</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	104 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	105 <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>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	106 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	107 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	108 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	109 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	110
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	111 </inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	112
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	113 <outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	114
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	115 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	116 <filter>outputs and 'outvcf' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	117 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	118 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	119 <filter>outputs and 'outgff' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	120 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	121 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	122 <filter>outputs and 'outtab' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	123 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	124 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	125 <filter>outputs and 'outsum' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	126 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	127 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	128 <filter>outputs and 'outlog' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	129 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	130 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	131 <filter>outputs and 'outaln' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	132 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	133 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	134 <filter>outputs and 'outcon' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	135 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	136 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	137 <filter>outputs and 'outbam' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	138 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	139 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	140 <filter>outputs and 'outzip' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	141 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	142
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	143 </outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	144
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	145 <tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	146
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	147 <test> <!-- test 0 - fasta ref no snps -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	148 <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	149 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	150 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	151 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	152 </conditional>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	153 <param name="fastq_input_selector" value="paired" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	154 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	155 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	156 <param name="mincov" value="2" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	157 <param name="minqual" value="60" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	158 <param name="outputs" value="outgff,outsum" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	159 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	160 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	161 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	162
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	163 <test> <!-- test 1 - fasta ref one snp -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	164 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	165 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	166 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	167 </conditional>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	168 <param name="fastq_input_selector" value="paired" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	169 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	170 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	171 <param name="mincov" value="2" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	172 <param name="minqual" value="60" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	173 <param name="outputs" value="outgff,outsum" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	174 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	175 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	176 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	177
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	178 <test> <!-- test 2 - fasta ref one snp paired_collection -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	179 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	180 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	181 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	182 </conditional>
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	183 <param name="fastq_input_selector" value="paired_collection" />
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	184 <param name="fastq_input">
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	185 <collection type="paired">
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	186 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	187 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	188 </collection>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	189 </param>
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	190 <param name="mincov" value="2" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	191 <param name="minqual" value="60" />
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	192 <param name="outputs" value="outgff,outsum" />
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	193 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	194 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
1 82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	195 </test>
82f2b6f20fa2 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	196
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	197 <test> <!-- test 3 - fasta ref one snp single -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	198 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	199 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	200 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	201 </conditional>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	202 <param name="fastq_input_selector" value="single" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	203 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	204 <param name="mincov" value="2" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	205 <param name="minqual" value="60" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	206 <param name="outputs" value="outgff,outsum" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	207 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	208 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	209 </test>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	210
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	211 <test> <!-- test 4 - reference source as cached -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	212 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	213 <param name="reference_source_selector" value="cached"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	214 <param name="ref_file" value="test_id"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	215 </conditional>
3 feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	216 <param name="fastq_input_selector" value="single" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	217 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	218 <param name="mincov" value="2" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	219 <param name="minqual" value="60" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	220 <param name="outputs" value="outgff,outsum" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	221 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	222 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
feb7e635c6af planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	223 </test>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	224 </tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	225
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	226
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	227 <help><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	228
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	229 Snippy @VERSION@
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	230
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	231 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	232
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	233 Author
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	234
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	235 Torsten Seemann
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	236
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	237 Inputs
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	238
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	239 - NGS Reads in fastq format (single or paired end)
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	240 - Reference file in either fasta or genbank format
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	241
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	242 If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	243
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	244 Advanced options
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	245
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	246 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	247
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	248 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	249
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	250 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	251
2 776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	252 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	253
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	254 - rgid - String - Use this @RG ID: in the BAM header (default '')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	255
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	256 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	257
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	258 Further information
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	259
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	260 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	261
5 0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	262 ]]> </help>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112" iuc parents: 3 diff changeset	263 <expand macro="citations"/>
0 c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	264
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	265 </tool>

Mercurial > repos > iuc > snippy

annotate snippy.xml @ 8:32f2211eeec3 draft