amplican: amplican.xml annotate

annotate amplican.xml @ 0:71adaaace336 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"

author	iuc
date	Wed, 22 Sep 2021 21:01:40 +0000
parents
children	8c1bba8d544a

rev	line source
0 71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	1 <tool id='amplican' name='AmpliCan' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	2 <description>analysis tool for genome editing </description>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	3 <macros>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	4 <import>macros.xml</import>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	5 </macros>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	6 <expand macro='requirements' />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	7 <expand macro="bio_tools"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	8 <command detect_errors='exit_code'><![CDATA[
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	9 #import re
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	10 mkdir ./fastq_folder ./output_folder
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	11 #for $i in $fastq_files
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	12 #if str($i.element_identifier) != re.sub('[^\w\-_\.]', '_', str($i.element_identifier))
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	13 && echo "Please rename your datasets; only underscore (_) and alphanumeric characters are allowed."
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	14 && exit 1
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	15 #else
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	16 && ln -s '${i}' ./fastq_folder/'${i.element_identifier}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	17 #end if
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	18 #end for
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	19 && Rscript '$amplican_script'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	20 #if 'knit_reports' in $output_options.outputs
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	21 && mv ./output_folder/reports/amplicon_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	22 && mv ./output_folder/reports/barcode_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	23 && mv ./output_folder/reports/group_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	24 && mv ./output_folder/reports/guide_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	25 && mv ./output_folder/reports/id_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	26 #end if
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	27 ]]> </command>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	28 <configfiles>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	29 <configfile name="amplican_script"><![CDATA[
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	30 ## Setup R error handling to go to stderr
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	31 options(
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	32 show.error.messages = F,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	33 error = function() {
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	34 cat(geterrmessage(), file = stderr())
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	35 q("no", 1, F)
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	36 }
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	37 )
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	38 # we need that to not crash galaxy with an UTF8 error on German LC settings.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	39 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	40
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	41 suppressPackageStartupMessages({
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	42 library("amplican")
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	43 })
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	44 #full analysis
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	45 amplicanPipeline(
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	46 '${config_file}',
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	47 'fastq_folder',
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	48 'output_folder',
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	49 #if 'knit_reports' in $output_options.outputs
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	50 knit_reports = TRUE,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	51 #else
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	52 knit_reports = FALSE,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	53 #end if
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	54 #if $output_options.write_alignment_format == 'fasta'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	55 write_alignments_format = "fasta",
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	56 #else if $output_options.write_alignment_format == 'txt'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	57 write_alignments_format = "txt",
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	58 #else
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	59 write_alignments_format = "None",
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	60 #end if
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	61 average_quality = $quality_options.average_quality,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	62 min_quality = $quality_options.min_quality,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	63 use_parallel = FALSE,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	64 scoring_matrix = Biostrings::nucleotideSubstitutionMatrix(
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	65 match = $alignment_options.scoring_matrix.match_scoring,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	66 mismatch = $alignment_options.scoring_matrix.mismatch_scoring,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	67 baseOnly = $alignment_options.scoring_matrix.base_only,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	68 type = "$alignment_options.scoring_matrix.scoring_type"
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	69 ),
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	70 gap_opening = $alignment_options.gap_opening,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	71 gap_extension = $alignment_options.gap_extension,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	72 fastqfiles = $advanced_options.fastq_use,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	73 primer_mismatch = $alignment_options.primer_mismatch,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	74 donor_mismatch = $alignment_options.donor_mismatch,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	75 PRIMER_DIMER = $advanced_options.primer_dimer,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	76 event_filter = $advanced_options.event_filter,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	77 cut_buffer = $advanced_options.cut_buffer,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	78 promiscuous_consensus = $advanced_options.promiscuous_consensus,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	79 normalize = c("guideRNA", "Group")
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	80 )
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	81 ]]></configfile>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	82 </configfiles>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	83 <inputs>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	84 <param name="config_file" type="data" format="txt" label="Configuration file"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	85 <param name="fastq_files" type="data" format="fastq, fastq.gz, fastqsanger, fastqsanger.gz"
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	86 multiple="true" label="FASTQ files"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	87 <section name="quality_options" title="Sequence quality options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	88 <param argument="average_quality" type="integer" min="0" max="93"
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	89 value="0" label="Average quality"
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	90 help="If the average quality of the reads fall below value of average_quality then sequence is filtered. Default is 0" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	91 <param argument="min_quality" type="integer" min="0" max="93"
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	92 value="20" label="Minimum quality"
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	93 help="If one of nucleotides has quality below min_quality, then the sequence is filtered. Default is 20" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	94 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	95 <section name="alignment_options" title="Alignment options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	96 <param argument="gap_opening" type="integer" min="0" max="40" value="25" label="Gap opening" help="The opening gap score" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	97 <param argument="gap_extension" type="integer" min="0" max="40" value="0" label="Gap extension" help="The gap extension score" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	98 <param argument="primer_mismatch" type="integer" min="0" max="40" value="0" label="Primer mismatch" help="Decide how many mismatches are allowed during primer matching of the reads, that groups reads by experiments. When primer_mismatch = 0 no mismatches are allowed, which can increase number of unasssigned read" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	99 <param argument="donor_mismatch" type="integer" min="0" max="40" value="3" label="Donor mismatch" help="How many events of length 1 (mismatches, deletions and insertions of length 1) are allowed when aligning toward the donor template. This parameter is only used when donor template is specified. The higher the parameter the less strict will be algorithm accepting read as HDR. Set to 0 if only perfect alignments to the donor template marked as HDR, unadvised due to error rate of the sequencers" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	100 <section name="scoring_matrix" title="Scoring matrix options" expanded="False">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	101 <param argument="match_scoring" type="integer" min="0" max="20" value="5" label="Match scoring" help="TODO" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	102 <param argument="mismatch_scoring" type="integer" min="-20" max="0" value="-4" label="Mismatch scoring" help="TODO" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	103 <param argument="base_only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Base only" help="TODO" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	104 <param argument="scoring_type" type="select" label="Scoring matrix type" help="TODO">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	105 <option value="DNA" selected="true">DNA</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	106 <option value="RNA">RNA</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	107 </param>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	108 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	109 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	110 <section name="advanced_options" title="Advanced options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	111 <param argument="fastq_use" type="select" label="FASTQ files to use" help="Normally you want to use both FASTQ files. But in some special cases, you may want to use only the forward file, or only the reverse file">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	112 <option value="0">Use both FASTQ files</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	113 <option value="0.5">Use both FASTQ files, but only for one of the reads (forward or reverse) is required to have primer perfectly matched to sequence</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	114 <option value="1">Use only the forward FASTQ file</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	115 <option value="2">Use only the reverse FASTQ file</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	116 </param>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	117 <param argument="primer_dimer" type="integer" min="0" max="50" value="30" label="Primer dimer" help="Value specifying buffer for PRIMER DIMER detection. For a given read it will be recognized as PRIMER DIMER when alignment will introduce gap of size bigger than: length of amplicon - (lengths of PRIMERS + PRIMER_DIMER value)" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	118 <param argument="event_filter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Event filter" help="Whether detection of offtarget reads, should be enabled" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	119 <param argument="cut_buffer" type="integer" min="0" max="30" value="5" label="Cut buffer" help="The number of bases by which extend expected cut sites (specified as UPPER case letters in the amplicon) in 5' and 3' directions" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	120 <param argument="promiscuous_consensus" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Promiscuous consensus" help="Whether rules of amplicanConsensus should be promiscuous. When promiscuous, we allow indels that have no confirmation on the other strand" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	121 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	122 <section name="output_options" title="Output options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	123 <param argument="write_alignment_format" type="select" label="Alignment format output" help="Whether it should write alignments results to separate files">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	124 <option value="None">None: don't write any alignments to files</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	125 <option value="txt" selected="true">Text file: read information followed by forward read and amplicon sequence followed by reverse read with its amplicon sequence</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	126 <option value="fasta">FASTA file: outputs alignments in fasta format where header indicates experiment ID, read id and number of reads</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	127 </param>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	128 <param name="outputs" type="select" label="Additional output files" display="checkboxes" multiple="true" help="Select the output files.">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	129 <option value="config_summary" selected="true">Configuration summary (config_summary.csv)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	130 <option value="barcode_reads" selected="true">Barcode reads filters (barcode_reads_filters.csv)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	131 <option value="knit_reports" selected="true" >Knitr HTML report</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	132 <option value="parameters" >Parameters (RunParameters.txt)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	133 <option value="alignments_rds" selected="true">Alignments Rda file (AlignmentsExperimentSet.rds)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	134 <option value="events_filtered_shifted" selected="true">Events filtered shifted (events_filtered_shifted.csv)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	135 <option value="events_filtered_shifted_normalized" selected="true">Events filtered shifted normalized (events_filtered_shifted_normalized.csv)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	136 <option value="raw_events" selected="true">Raw events (raw_events.csv)</option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	137 <option value="unassigned_reads" selected="true">Unnasigned reads (unassigned_reads.csv) </option>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	138 </param>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	139 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	140 </inputs>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	141 <outputs>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	142 <data name="config_summary" from_work_dir="./output_folder/config_summary.csv" format="csv" label="${tool.name} on ${on_string}: config summary">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	143 <filter>"config_summary" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	144 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	145 <data name="barcode_reads" from_work_dir="./output_folder/barcode_reads_filters.csv" format="tabular" label="${tool.name} on ${on_string}: barcode reads filters">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	146 <filter>"barcode_reads" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	147 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	148 <data name="output_html" from_work_dir="./output_folder/reports/index.html" format="html" label="${tool.name} on ${on_string}: report">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	149 <filter>"knit_reports" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	150 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	151 <data name="parameters" from_work_dir="./output_folder/RunParameters.txt" format="txt" label="${tool.name} on ${on_string}: run parameters">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	152 <filter>"parameters" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	153 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	154 <data name="alignments_rds" from_work_dir="./output_folder/alignments/AlignmentsExperimentSet.rds" format="rdata" label="${tool.name} on ${on_string}: alignments experiment set">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	155 <filter>"alignments_rds" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	156 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	157 <data name="alignments_fasta" from_work_dir="./output_folder/alignments/alignments.fasta" format="fasta" label="${tool.name} on ${on_string}: alignments (FASTA)">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	158 <filter>output_options["write_alignment_format"] == "fasta"</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	159 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	160 <data name="alignments_txt" from_work_dir="./output_folder/alignments/alignments.txt" format="txt" label="${tool.name} on ${on_string}: alignments (txt)">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	161 <filter>output_options["write_alignment_format"] == "txt"</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	162 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	163 <data name="events_filtered_shifted" from_work_dir="./output_folder/alignments/events_filtered_shifted.csv" format="csv" label="${tool.name} on ${on_string}: evens filtered shifted">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	164 <filter>"events_filtered_shifted" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	165 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	166 <data name="events_filtered_shifted_normalized" from_work_dir="./output_folder/alignments/events_filtered_shifted_normalized.csv" format="csv" label="${tool.name} on ${on_string}: events filtered shifted normalized">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	167 <filter>"events_filtered_shifted_normalized" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	168 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	169 <data name="raw_events" from_work_dir="./output_folder/alignments/raw_events.csv" format="csv" label="${tool.name} on ${on_string}: raw events">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	170 <filter>"raw_events" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	171 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	172 <data name="unassigned_reads" from_work_dir="./output_folder/alignments/unassigned_reads.csv" format="csv" label="${tool.name} on ${on_string}: unnasigned reads">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	173 <filter>"unassigned_reads" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	174 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	175 </outputs>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	176 <tests>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	177 <!-- Test default inputs -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	178 <test expect_num_outputs="10">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	179 <param name="config_file" value="config.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	180 <param name="fastq_files" value="R1_001.fastq,R1_002.fastq,R2_001.fastq,R2_002.fastq" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	181 <section name="quality_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	182 <param name="average_quality" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	183 <param name="min_quality" value="20"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	184 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	185 <section name="alignment_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	186 <param name="gap_opening" value="25"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	187 <param name="gap_extension" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	188 <param name="primer_mismatch" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	189 <param name="donor_mismatch" value="3"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	190 <section name="scoring_matrix">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	191 <param name="match_scoring" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	192 <param name="mismatch scoring" value="-4"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	193 <param name="base_only" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	194 <param name="scoring_type" value="DNA"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	195 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	196 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	197 <section name="advanced_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	198 <param name="fastq_use" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	199 <param name="primer_dimer" value="30"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	200 <param name="event_filter" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	201 <param name="cut_buffer" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	202 <param name="promiscuous_consensus" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	203 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	204 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	205 <param name="write_alignment_format" value="txt"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	206 <param name="outputs" value="config_summary,barcode_reads,knit_reports,parameters,alignments_rds,events_filtered_shifted,events_filtered_shifted_normalized,raw_events,unassigned_reads"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	207 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	208 <output name="config_summary" file="config_summary.csv" ftype="csv" lines_diff="10">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	209 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	210 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	211 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	212 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	213 <output name="barcode_reads" file="barcode_reads_filtered.csv" ftype="tabular">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	214 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	215 <has_size value="212" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	216 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	217 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	218 <output name="output_html" file="output_html.html" ftype="html" lines_diff="17">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	219 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	220 <has_size value="1641557" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	221 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	222 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	223 <output name="parameters" file="RunParameters.txt" ftype="txt" lines_diff="4">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	224 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	225 <has_size value="418" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	226 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	227 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	228 <output name="alignments_rds" ftype="rdata">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	229 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	230 <has_size value="86527" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	231 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	232 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	233 <output name="alignments_txt" file="alignments.txt" ftype="txt">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	234 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	235 <has_size value="13406" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	236 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	237 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	238 <output name="events_filtered_shifted" file="events_filtered_shifted.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	239 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	240 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	241 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	242 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	243 <output name="events_filtered_shifted_normalized" file="events_filtered_shifted_normalized.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	244 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	245 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	246 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	247 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	248 <output name="raw_events" file="raw_events.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	249 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	250 <has_size value="4455" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	251 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	252 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	253 <output name="unassigned_reads" file="unassigned_reads.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	254 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	255 <has_size value="1176" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	256 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	257 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	258 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	259 <!-- Test alignment output in fasta format -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	260 <test expect_num_outputs="10">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	261 <param name="config_file" value="config.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	262 <param name="fastq_files" value="R1_001.fastq,R1_002.fastq,R2_001.fastq,R2_002.fastq" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	263 <section name="quality_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	264 <param name="average_quality" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	265 <param name="min_quality" value="20"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	266 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	267 <section name="alignment_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	268 <param name="gap_opening" value="25"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	269 <param name="gap_extension" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	270 <param name="primer_mismatch" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	271 <param name="donor_mismatch" value="3"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	272 <section name="scoring_matrix">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	273 <param name="match_scoring" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	274 <param name="mismatch scoring" value="-4"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	275 <param name="base_only" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	276 <param name="scoring_type" value="DNA"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	277 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	278 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	279 <section name="advanced_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	280 <param name="fastq_use" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	281 <param name="primer_dimer" value="30"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	282 <param name="event_filter" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	283 <param name="cut_buffer" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	284 <param name="promiscuous_consensus" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	285 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	286 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	287 <param name="write_alignment_format" value="fasta"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	288 <param name="outputs" value="config_summary,barcode_reads,knit_reports,parameters,alignments_rds,events_filtered_shifted,events_filtered_shifted_normalized,raw_events,unassigned_reads"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	289 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	290 <output name="config_summary" ftype="csv" >
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	291 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	292 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	293 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	294 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	295 <output name="barcode_reads" ftype="tabular">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	296 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	297 <has_size value="212" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	298 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	299 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	300 <output name="output_html" ftype="html">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	301 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	302 <has_size value="1641557" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	303 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	304 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	305 <output name="parameters" ftype="txt" lines_diff="2">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	306 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	307 <has_size value="418" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	308 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	309 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	310 <output name="alignments_rds" ftype="rdata">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	311 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	312 <has_size value="86527" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	313 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	314 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	315 <output name="alignments_fasta" ftype="fasta">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	316 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	317 <has_size value="16146" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	318 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	319 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	320 <output name="events_filtered_shifted" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	321 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	322 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	323 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	324 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	325 <output name="events_filtered_shifted_normalized" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	326 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	327 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	328 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	329 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	330 <output name="raw_events" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	331 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	332 <has_size value="4455" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	333 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	334 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	335 <output name="unassigned_reads" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	336 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	337 <has_size value="1176" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	338 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	339 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	340 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	341 <!-- Test limit outputs -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	342 <test expect_num_outputs="2">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	343 <param name="config_file" value="config.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	344 <param name="fastq_files" value="R1_001.fastq,R1_002.fastq,R2_001.fastq,R2_002.fastq" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	345 <section name="quality_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	346 <param name="average_quality" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	347 <param name="min_quality" value="20"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	348 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	349 <section name="alignment_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	350 <param name="gap_opening" value="25"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	351 <param name="gap_extension" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	352 <param name="primer_mismatch" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	353 <param name="donor_mismatch" value="3"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	354 <section name="scoring_matrix">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	355 <param name="match_scoring" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	356 <param name="mismatch scoring" value="-4"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	357 <param name="base_only" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	358 <param name="scoring_type" value="DNA"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	359 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	360 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	361 <section name="advanced_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	362 <param name="fastq_use" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	363 <param name="primer_dimer" value="30"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	364 <param name="event_filter" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	365 <param name="cut_buffer" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	366 <param name="promiscuous_consensus" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	367 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	368 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	369 <param name="write_alignment_format" value="fasta"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	370 <param name="outputs" value="config_summary"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	371 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	372 <output name="config_summary" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	373 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	374 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	375 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	376 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	377 <output name="alignments_fasta" ftype="fasta">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	378 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	379 <has_size value="16146" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	380 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	381 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	382 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	383 <!-- Test gzip files -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	384 <test expect_num_outputs="2">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	385 <param name="config_file" value="config_gzip.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	386 <param name="fastq_files" value="R1_001.fastq.gz,R1_002.fastq.gz,R2_001.fastq.gz,R2_002.fastq.gz" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	387 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	388 <param name="write_alignment_format" value="fasta"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	389 <param name="outputs" value="config_summary"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	390 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	391 <output name="config_summary" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	392 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	393 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	394 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	395 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	396 <output name="alignments_fasta" ftype="fasta">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	397 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	398 <has_size value="16146" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	399 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	400 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	401 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	402 </tests>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	403 <help><![CDATA[
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	404 .. class:: infomark
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	405
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	406 Purpose
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	407
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	408 AmpliCan is an analysis tool for genome editing that unites highly precise quantification and
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	409 visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	410 filtering of experimental artifacts, event-specific normalization, and off-target read detection
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	411 and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	412 scalable to thousands of amplicon sequencing-based experiments from any genome editing experiment,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	413 including CRISPR. It enables automated integration of controls and accounts for biases at every
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	414 step of the analysis.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	415
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	416 ----
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	417
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	418 .. class:: infomark
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	419
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	420 Config file details
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	421
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	422 Columns of the config file:
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	423
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	424 - ID - should be a unique identifier of your experiments.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	425 - Barcode - use this to group experiments with the same barcode.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	426 - Forward_Reads, Reverse_Reads - put names of your files in these fields, you can put here files compressed to .gz, we will unpack them for you.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	427 - Group - use this field if you want to group ID by other criteria, here for instance we will group by person that performed experiment, on later stage it is possible to generate report with breakdown using this field.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	428 - guideRNA - put your guideRNA in 5’ to 3’ fashion here, if he has to be reverse complemented to be found in the amplicon put “1” into Direction field, we will use this field to make sure your guideRNA is inside the amplicon and during plotting of the results.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	429 - Forward_Primer, Reverse_Primer - make sure these primers are correct for each of your IDs, Forward_Primer should be found in the amplicon as is, on the left side of the guide, Reverse_Primer reverse complement should be found on the amplicon on the right side of the guide.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	430 - Direction - here “0” means guide does not requires to be reverse complemented to be matched to the amplicon, “1” means it should be reverse complemented, this field is also used when plotting deletions, mismatches and insertions.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	431 - Amplicon - insert amplicon sequence as lower case letters, by putting UPPER CASE letters you can specify expected cut site, you should specify at least one cut site, here for example we specify in uppercase letter PAM sequence of the corresponding guideRNA.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	432 - Donor - insert donor template if you have designed HDR experiments or used base editors, otherwise leave empty, but keep the column. amplican will estimate HDR efficiency based on the events from aligning donor and amplicon sequences, donor and reads and reads and amplicon.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	433
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	434 If you have only forward primers leave column Reverse_Primer empty, leave empty also the Reverse_Reads column. You can still use amplican like normal.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	435
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	436 ]]> </help>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	437 <expand macro="citations" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" iuc parents: diff changeset	438 </tool>

Mercurial > repos > iuc > amplican

annotate amplican.xml @ 0:71adaaace336 draft