Mercurial > repos > nml > ectyper

comparison ectyper.xml @ 1:b02c775b27c8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
author nml
date Thu, 31 Jan 2019 09:39:04 -0500
parents b60c187a3a02
children e79a8dad83b4
comparison
equal deleted inserted replaced
0:b60c187a3a02 1:b02c775b27c8
17 #end for 17 #end for
18 #else 18 #else
19 ln -s "${input}" "${input.name}" && 19 ln -s "${input}" "${input.name}" &&
20 #set $genomes = $input.name 20 #set $genomes = $input.name
21 #end if 21 #end if
22
23 #if $mash_input
24 ln -s "${mash_input}" mash_sketch.msh &&
25 #end if
22 26
23 ectyper --cores \${GALAXY_SLOTS:-4} 27 ectyper --cores \${GALAXY_SLOTS:-4}
24 --input "${genomes}" 28 --input "${genomes}"
25 --percentIdentity '$adv_param.min_percentIdentity' 29 --percentIdentity '$adv_param.min_percentIdentity'
26 --percentLength '$adv_param.percentLength' 30 --percentLength '$adv_param.percentLength'
27 #if $adv_param.verifyEcoli 31 #if $adv_param.verifyEcoli
28 --verify 32 --verify
29 #end if 33 #end if
34 #if $mash_input
35 --refseq mash_sketch.msh
36 #end if
30 #if $adv_param.alleleSequence 37 #if $adv_param.alleleSequence
31 --sequence 38 --sequence
32 #end if 39 #end if
33 --output '.' 40 --output '.'
34 ]]> 41 ]]>
35 </command> 42 </command>
36 <inputs> 43 <inputs>
37 <param name="input" type="data" format="fastq,fasta" label="Input(s)" help="FASTA or FASTQ file(s) with contig(s)"/> 44 <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s) with contig(s)"/>
45 <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide MASH sketches to find closest genome (in case O/H typing fails)"/>
38 <section name="adv_param" title="Advanced parameters" expanded="False"> 46 <section name="adv_param" title="Advanced parameters" expanded="False">
39 <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/> 47 <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
40 <param name="percentLength" type="integer" value="50" min="1" max="100"/> 48 <param name="percentLength" type="integer" value="50" min="1" max="100"/>
41 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/> 49 <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
42 <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/> 50 <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/>
73 81
74 ----- 82 -----
75 83
76 **Input:** 84 **Input:**
77 85
78 Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended. 86 Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended.
79 87
88 Optionally select a MASH RefSeq genome sketch (version 2.0 and above) for cases when O/H typing would fail. Download RefSeq genome sketch containing 91,283 genomes with 1000 hashes each directly from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh .
80 89
81 **Output:** 90 **Output:**
82 91
83 Tab-delimited report listing identified O and H antigens together with corresponding highest scoring alleles and normalized BLAST score defined as (%identity x query coverage length) / 10000 92 Tab-delimited report listing identified O and H antigens together with corresponding highest scoring alleles and normalized BLAST score defined as (%identity x query coverage length) / 10000
84 93