snippy: snippy.xml annotate

annotate snippy.xml @ 9:43791d945de1 draft

"planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7"

author	iuc
date	Sun, 01 Dec 2019 18:05:33 +0000
parents	eea223efd86e
children	a3f95a688c47

rev	line source
9 43791d945de1 "planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7" iuc parents: 8 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.
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	4 </description>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	5 <macros>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	6 <import>macros.xml</import>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	7 </macros>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	8 <expand macro="requirements" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	9 <expand macro="version_command" />
0 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
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	13 @REFERENCE_SOURCE_FILE@
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	14
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	15 snippy
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	16 --outdir 'out'
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	17 --cpus \${GALAXY_SLOTS:-1}
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	18 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	19 @REFERENCE_COMMAND@
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	20 --mapqual $adv.mapqual
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	21 --mincov $adv.mincov
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	22 --minfrac $adv.minfrac
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	23 --minqual $adv.minqual
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	24 #if $adv.rgid
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	25 --rgid '$adv.rgid'
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	26 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	27 #if $adv.bwaopt
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	28 --bwaopt '$adv.bwaopt'
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	29 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	30
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	31 #if str( $fastq_input.fastq_input_selector ) == "paired"
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	32 --R1 '$fastq_input.fastq_input1'
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	33 --R2 '$fastq_input.fastq_input2'
3 a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	34 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	35 --R1 '$fastq_input.fastq_input.forward'
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	36 --R2 '$fastq_input.fastq_input.reverse'
3 a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	37 #elif str( $fastq_input.fastq_input_selector ) == "single"
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	38 --se '$fastq_input.fastq_input_single'
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	39 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	40 --peil '$fastq_input.fastq_input_interleaved'
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	41 #end if
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	42
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	43 &&
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	44
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	45 #import re
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	46 #if str( $fastq_input.fastq_input_selector ) == "paired"
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	47 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	48 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	49 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
3 a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	50 #elif str( $fastq_input.fastq_input_selector ) == "single"
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	51 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	53 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	54 #end if
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	55
2 4eb9595bff60 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}/ &&
9 43791d945de1 "planemo upload commit 5b41fad964a75dcdc794e90342144c3eccea16d7" iuc parents: 8 diff changeset	57 tar -czf out.tgz ${dir_name}
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	58 #if "outcon" in str($outputs) and $adv.rename_cons
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	59 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	60 #end if
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	61
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	62
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	63 ]]> </command>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	64
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	65 <inputs>
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	66 <expand macro="reference_selector" />
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	67 <conditional name="fastq_input">
ff177a01b5ca 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">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	69 <option value="paired">Paired</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	70 <option value="single">Single</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	71 <option value="paired_collection">Paired Collection</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	72 <option value="paired_iv">Paired Interleaved</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	73 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	74 <when value="paired">
ff177a01b5ca 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"/>
ff177a01b5ca 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"/>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	77 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	78 <when value="single">
3 a2147b3769dd 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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	80 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	81 <when value="paired_collection">
1 d4e6df2bc5e8 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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	83 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	84 <when value="paired_iv">
3 a2147b3769dd 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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	86 </when>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	87 </conditional>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	88
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	89 <section name="adv" title="Advanced parameters" expanded="false">
ff177a01b5ca 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" />
ff177a01b5ca 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" />
ff177a01b5ca 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 4eb9595bff60 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 ff177a01b5ca 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" />
ff177a01b5ca 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 4eb9595bff60 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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	97 </section>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	98
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	99 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	100 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	101 <option value="outgff" selected="False">The variants in GFF3 format</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	102 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	103 <option value="outsum" selected="False">A summary of the samples and mapping</option>
ff177a01b5ca 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>
ff177a01b5ca 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>
ff177a01b5ca 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>
ff177a01b5ca 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>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	108 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	109 </param>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	110
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	111 </inputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	112
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	113 <outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	114
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	115 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	116 <filter>outputs and 'outvcf' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	117 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	118 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	119 <filter>outputs and 'outgff' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	120 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	121 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	122 <filter>outputs and 'outtab' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	123 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	124 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	125 <filter>outputs and 'outsum' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	126 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	127 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	128 <filter>outputs and 'outlog' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	129 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	130 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	131 <filter>outputs and 'outaln' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	132 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	133 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	134 <filter>outputs and 'outcon' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	135 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	136 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	137 <filter>outputs and 'outbam' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	138 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	139 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	140 <filter>outputs and 'outzip' in outputs</filter>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	141 </data>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	142
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	143 </outputs>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	144
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	145 <tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	146
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	147 <test> <!-- test 0 - fasta ref no snps -->
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	148 <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	149 <conditional name="reference_source">
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	150 <param name="reference_source_selector" value="history"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	151 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	152 </conditional>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	153 <param name="fastq_input_selector" value="paired" />
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	154 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	155 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	156 <param name="mincov" value="2" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	157 <param name="minqual" value="60" />
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	158 <param name="outputs" value="outgff,outsum" />
2 4eb9595bff60 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" />
4eb9595bff60 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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	161 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	162
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	163 <test> <!-- test 1 - fasta ref one snp -->
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	164 <conditional name="reference_source">
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	165 <param name="reference_source_selector" value="history"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	166 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	167 </conditional>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	168 <param name="fastq_input_selector" value="paired" />
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	169 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	170 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	171 <param name="mincov" value="2" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	172 <param name="minqual" value="60" />
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	173 <param name="outputs" value="outgff,outsum" />
2 4eb9595bff60 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" />
4eb9595bff60 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 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	176 </test>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	177
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	178 <test> <!-- test 2 - fasta ref one snp paired_collection -->
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	179 <conditional name="reference_source">
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	180 <param name="reference_source_selector" value="history"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	181 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	182 </conditional>
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	183 <param name="fastq_input_selector" value="paired_collection" />
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	184 <param name="fastq_input">
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	185 <collection type="paired">
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	186 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	187 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	188 </collection>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	189 </param>
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	190 <param name="mincov" value="2" />
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	191 <param name="minqual" value="60" />
1 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	192 <param name="outputs" value="outgff,outsum" />
2 4eb9595bff60 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" />
4eb9595bff60 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 d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	195 </test>
d4e6df2bc5e8 planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 iuc parents: 0 diff changeset	196
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	197 <test> <!-- test 3 - fasta ref one snp single -->
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	198 <conditional name="reference_source">
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	199 <param name="reference_source_selector" value="history"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	200 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	201 </conditional>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	202 <param name="fastq_input_selector" value="single" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	203 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	204 <param name="mincov" value="2" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	205 <param name="minqual" value="60" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	206 <param name="outputs" value="outgff,outsum" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	207 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	208 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	209 </test>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	210
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	211 <test> <!-- test 4 - reference source as cached -->
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	212 <conditional name="reference_source">
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	213 <param name="reference_source_selector" value="cached"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	214 <param name="ref_file" value="test_id"/>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	215 </conditional>
3 a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	216 <param name="fastq_input_selector" value="single" />
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	217 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	218 <param name="mincov" value="2" />
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	219 <param name="minqual" value="60" />
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	220 <param name="outputs" value="outgff,outsum" />
a2147b3769dd 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" />
a2147b3769dd 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" />
a2147b3769dd planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308 iuc parents: 2 diff changeset	223 </test>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	224 </tests>
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	225
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	226
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	227 <help><![CDATA[
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	228
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	229 Snippy @VERSION@
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	230
ff177a01b5ca 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).
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	232
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	233 Author
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	234
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	235 Torsten Seemann
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	236
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	237 Inputs
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	238
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	239 - NGS Reads in fastq format (single or paired end)
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	240 - Reference file in either fasta or genbank format
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	241
ff177a01b5ca 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.
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	243
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	244 Advanced options
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	245
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	246 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	247
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	248 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	249
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	250 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	251
2 4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	252 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
4eb9595bff60 planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496 iuc parents: 1 diff changeset	253
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	254 - rgid - String - Use this @RG ID: in the BAM header (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	255
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	256 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	257
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	258 Further information
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	259
ff177a01b5ca 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
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	261
5 f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	262 ]]> </help>
f9d3b5a6ef31 "planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2" iuc parents: 3 diff changeset	263 <expand macro="citations"/>
0 ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	264
ff177a01b5ca planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 iuc parents: diff changeset	265 </tool>

Mercurial > repos > iuc > snippy

annotate snippy.xml @ 9:43791d945de1 draft